dbSNP rs1165678: ENSG00000293399:n.272+1476C>T (chr12-103928406-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 ENST00000388789.5(ENSG00000293399):n.272+1476C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,072 control chromosomes in the GnomAD database, including 34,721 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 0.67 ( 34711 hom., cov: 32)

Exomes 𝑓: 0.67 ( 10 hom. )

Consequence

ENSG00000293399
ENST00000388789.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.07

Publications

5 publications found

Variant links:

Genes affected

ENSG00000293399 (HGNC:):

ENSG00000293399 links:

TTC41P (HGNC:49210): (tetratricopeptide repeat domain 41, pseudogene) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TTC41P links:

Genome browser will be placed here

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=-0.57).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC41P	NR_027249.1 link	n.330+1476C>T		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293399	ENST00000388789.5 link	n.272+1476C>T	intron_variant	Intron 1 of 1	1
ENSG00000293399	ENST00000548897.1 link	n.471C>T	non_coding_transcript_exon_variant	Exon 2 of 5	5
ENSG00000293399	ENST00000848162.1 link	n.352C>T	non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.670

AC:

101730

AN:

151908

Hom.:

34672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.750

Gnomad AMI

AF:

0.728

Gnomad AMR

AF:

0.712

Gnomad ASJ

AF:

0.695

Gnomad EAS

AF:

0.848

Gnomad SAS

AF:

0.834

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.684

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.641

GnomAD4 exome

AF:

0.674

AC:

AN:

Hom.:

Cov.:

AF XY:

0.694

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.656

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.552

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.670

AC:

101830

AN:

152026

Hom.:

34711

Cov.:

AF XY:

0.676

AC XY:

50244

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.750

AC:

31074

AN:

41456

American (AMR)

AF:

0.713

AC:

10881

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.695

AC:

2413

AN:

3470

East Asian (EAS)

AF:

0.848

AC:

4381

AN:

5168

South Asian (SAS)

AF:

0.835

AC:

4022

AN:

4818

European-Finnish (FIN)

AF:

0.600

AC:

6340

AN:

10560

Middle Eastern (MID)

AF:

0.663

AC:

195

AN:

294

European-Non Finnish (NFE)

AF:

0.596

AC:

40502

AN:

67978

Other (OTH)

AF:

0.646

AC:

1361

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1663

3325

4988

6650

8313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<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:

0.649

Hom.:

4701

Bravo

AF:

0.680

Asia WGS

AF:

0.835

AC:

2902

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

2.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over