10-713328-A-G

Variant names:

• chr10-713328-A-G
• rs7916968

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 0.126 in 152,166 control chromosomes in the GnomAD database, including 1,294 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 0.13 (1294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.126 AC: 19150 AN: 152048 Hom.: 1287 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.126 AC: 19187 AN: 152166 Hom.: 1294 Cov.: 32 AF XY: 0.128 AC XY: 9510 AN XY: 74418

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0941

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0988 Hom.: 1164

Bravo AF: 0.131

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7916968; hg19: chr10-759268;