rs7916940

Positions:

• chr10-121436796-A-G

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 0.645 in 151,986 control chromosomes in the GnomAD database, including 32,115 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 0.64 (32115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97961 AN: 151868 Hom.: 32090 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.645 AC: 98030 AN: 151986 Hom.: 32115 Cov.: 32 AF XY: 0.643 AC XY: 47762 AN XY: 74272

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.642

Alfa AF: 0.678 Hom.: 10768

Bravo AF: 0.628

Asia WGS AF: 0.621 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7916940; hg19: chr10-123196310;