rs10008257

Variant names:

• chr4-94435177-G-A
• rs10008257

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 0.617 in 152,066 control chromosomes in the GnomAD database, including 30,341 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 0.62 (30341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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: 0.617 AC: 93769 AN: 151948 Hom.: 30283 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.617 AC: 93887 AN: 152066 Hom.: 30341 Cov.: 32 AF XY: 0.613 AC XY: 45550 AN XY: 74320

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.608

Alfa AF: 0.551 Hom.: 20237

Bravo AF: 0.640

Asia WGS AF: 0.434 AC: 1508 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10008257; hg19: chr4-95356328;