dbSNP rs10518603: ENSG00000251598:n.182-11422G>T (chr4-132039903-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000420721.2(ENSG00000251598):n.182-11422G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 151,968 control chromosomes in the GnomAD database, including 947 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 0.10 ( 947 hom., cov: 32)

Consequence

ENSG00000251598
ENST00000420721.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.93

Publications

1 publications found

Variant links:

Genes affected

ENSG00000251598 (HGNC:):

ENSG00000251598 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377428	XR_939203.4 link	n.77-5947G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251598	ENST00000420721.2 link	n.182-11422G>T		intron_variant	Intron 1 of 2	4
ENSG00000251598	ENST00000652009.1 link	n.178-11422G>T		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15208

AN:

151850

Hom.:

939

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.0824

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.0705

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0802

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0721

Gnomad OTH

AF:

0.102

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

GnomAD4 genome

AF:

0.100

AC:

15248

AN:

151968

Hom.:

947

Cov.:

AF XY:

0.100

AC XY:

7442

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.161

AC:

6688

AN:

41450

American (AMR)

AF:

0.0825

AC:

1257

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

357

AN:

3468

East Asian (EAS)

AF:

0.0705

AC:

365

AN:

5176

South Asian (SAS)

AF:

0.113

AC:

545

AN:

4810

European-Finnish (FIN)

AF:

0.0802

AC:

850

AN:

10592

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0721

AC:

4897

AN:

67912

Other (OTH)

AF:

0.102

AC:

216

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

699

1398

2096

2795

3494

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.0819

Hom.:

288

Bravo

AF:

0.102

Asia WGS

AF:

0.0890

AC:

312

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.32

(source)

DANN

Benign

0.62

PhyloP100

-1.9

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