rs10017149

Variant names:

• chr4-61083343-A-G
• rs10017149

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.501 in 151,588 control chromosomes in the GnomAD database, including 20,685 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 0.50 (20685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.502 AC: 75967 AN: 151470 Hom.: 20681 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.501 AC: 76001 AN: 151588 Hom.: 20685 Cov.: 31 AF XY: 0.494 AC XY: 36562 AN XY: 74060

African (AFR) AF: 0.314 AC: 13002 AN: 41378

American (AMR) AF: 0.459 AC: 6955 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2081 AN: 3460

East Asian (EAS) AF: 0.241 AC: 1247 AN: 5164

South Asian (SAS) AF: 0.549 AC: 2650 AN: 4824

European-Finnish (FIN) AF: 0.527 AC: 5538 AN: 10518

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42886 AN: 67788

Other (OTH) AF: 0.502 AC: 1054 AN: 2098

Alfa AF: 0.535 Hom.: 3425

Bravo AF: 0.484

Asia WGS AF: 0.364 AC: 1262 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10017149; hg19: chr4-61949061;