dbSNP rs3842729: ENSG00000295384:n.174+4192G>A (chr11-2163106-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 ENST00000729705.1(ENSG00000295384):n.174+4192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,178 control chromosomes in the GnomAD database, including 2,097 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 0.15 ( 2097 hom., cov: 33)

Consequence

ENSG00000295384
ENST00000729705.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.89

Publications

8 publications found

Variant links:

COSMIC-nc: COSV51746785

Genes affected

ENSG00000295384 (HGNC:):

ENSG00000295384 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295384	ENST00000729705.1 link	n.174+4192G>A		intron_variant	Intron 1 of 2
ENSG00000295384	ENST00000729706.1 link	n.225+4192G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22524

AN:

152060

Hom.:

2096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0413

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.0345

Gnomad SAS

AF:

0.128

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.129

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.148

AC:

22522

AN:

152178

Hom.:

2097

Cov.:

AF XY:

0.143

AC XY:

10666

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0412

AC:

1710

AN:

41548

American (AMR)

AF:

0.154

AC:

2349

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

738

AN:

3472

East Asian (EAS)

AF:

0.0344

AC:

178

AN:

5170

South Asian (SAS)

AF:

0.128

AC:

618

AN:

4824

European-Finnish (FIN)

AF:

0.155

AC:

1641

AN:

10606

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14710

AN:

67946

Other (OTH)

AF:

0.127

AC:

268

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

995

1990

2985

3980

4975

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.182

Hom.:

458

Bravo

AF:

0.142

Asia WGS

AF:

0.0880

AC:

306

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.4

(source)

DANN

Benign

0.55

PhyloP100

-3.9

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over