dbSNP rs2273553: TCP11L1:c.352+3678G>A (chr11-33076331-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000528962.1(TCP11L1):c.352+3678G>A variant causes a intron change. The variant allele was found at a frequency of 0.144 in 1,438,182 control chromosomes in the GnomAD database, including 16,294 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1573 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14721 hom. )

Consequence

TCP11L1
ENST00000528962.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.60

Publications

9 publications found

Variant links:

Genes affected

TCP11L1 (HGNC:25655): (t-complex 11 like 1) Predicted to be involved in signal transduction. Located in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

TCP11L1 links:

PIGCP1 (HGNC:8961): (phosphatidylinositol glycan anchor biosynthesis class C pseudogene 1)

PIGCP1 links:

LINC00294 (HGNC:27456): (long intergenic non-protein coding RNA 294)

LINC00294 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000528962.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528962.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00294	NR_015451.1		n.182G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TCP11L1	ENST00000528962.1	TSL:3	c.352+3678G>A	intron	N/A	ENSP00000436471.1	H0YES4
PIGCP1	ENST00000527583.1	TSL:6	n.130C>T	non_coding_transcript_exon	Exon 1 of 1
LINC00294	ENST00000631190.1	TSL:6	n.183G>A	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20321

AN:

152046

Hom.:

1576

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0584

Gnomad AMI

AF:

0.178

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.119

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.155

GnomAD4 exome

AF:

0.145

AC:

186329

AN:

1286018

Hom.:

14721

Cov.:

AF XY:

0.146

AC XY:

94459

AN XY:

648026

show subpopulations

African (AFR)

AF:

0.0473

AC:

1457

AN:

30798

American (AMR)

AF:

0.117

AC:

5192

AN:

44230

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

5358

AN:

24744

East Asian (EAS)

AF:

0.111

AC:

4316

AN:

38832

South Asian (SAS)

AF:

0.112

AC:

9298

AN:

83080

European-Finnish (FIN)

AF:

0.167

AC:

8715

AN:

52126

Middle Eastern (MID)

AF:

0.195

AC:

1059

AN:

5428

European-Non Finnish (NFE)

AF:

0.150

AC:

142696

AN:

952608

Other (OTH)

AF:

0.152

AC:

8238

AN:

54172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.427

Heterozygous variant carriers

6431

12863

19294

25726

32157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4488

8976

13464

17952

22440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.133

AC:

20311

AN:

152164

Hom.:

1573

Cov.:

AF XY:

0.132

AC XY:

9826

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0582

AC:

2419

AN:

41532

American (AMR)

AF:

0.138

AC:

2103

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

791

AN:

3468

East Asian (EAS)

AF:

0.118

AC:

610

AN:

5168

South Asian (SAS)

AF:

0.100

AC:

483

AN:

4824

European-Finnish (FIN)

AF:

0.164

AC:

1740

AN:

10578

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11614

AN:

67990

Other (OTH)

AF:

0.154

AC:

324

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

886

1772

2658

3544

4430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

226

452

678

904

1130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.123

Hom.:

229

Bravo

AF:

0.131

Asia WGS

AF:

0.0820

AC:

285

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

6.1

(source)

DANN

Benign

0.67

PhyloP100

3.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over