rs10008257

Positions:

• chr4-94435177-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;