rs10958704

Variant names:

• chr8-38470784-A-G
• rs10958704

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 0.351 in 152,036 control chromosomes in the GnomAD database, including 9,779 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 0.35 (9779 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 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: 0.351 AC: 53379 AN: 151918 Hom.: 9771 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.351 AC: 53393 AN: 152036 Hom.: 9779 Cov.: 32 AF XY: 0.353 AC XY: 26238 AN XY: 74310

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.332

Alfa AF: 0.385 Hom.: 3112

Bravo AF: 0.333

Asia WGS AF: 0.430 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10958704; hg19: chr8-38328302;