rs10503961

Positions:

• chr8-34352750-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 0.0574 in 152,210 control chromosomes in the GnomAD database, including 337 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 0.057 (337 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34352750G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8741 AN: 152092 Hom.: 337 Cov.: 33

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0691

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0840

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0574 AC: 8741 AN: 152210 Hom.: 337 Cov.: 33 AF XY: 0.0556 AC XY: 4134 AN XY: 74410

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.0691

Gnomad4 NFE AF: 0.0841

Gnomad4 OTH AF: 0.0722

Alfa AF: 0.0763 Hom.: 247

Bravo AF: 0.0550

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503961; hg19: chr8-34210268;