rs10017149

Variant names:

• chr4-61083343-A-G
• rs10017149

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.502

Alfa AF: 0.544 Hom.: 3386

Bravo AF: 0.484

Asia WGS AF: 0.364 AC: 1262 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10017149; hg19: chr4-61949061;