rs10017149

chr4-61083343-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;