rs10953645

Variant names:

• chr7-109873860-G-A
• rs10953645

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 0.358 in 151,884 control chromosomes in the GnomAD database, including 10,573 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 0.36 (10573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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: 0.358 AC: 54374 AN: 151766 Hom.: 10575 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.358 AC: 54391 AN: 151884 Hom.: 10573 Cov.: 32 AF XY: 0.357 AC XY: 26488 AN XY: 74242

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.391

Alfa AF: 0.422 Hom.: 18878

Bravo AF: 0.340

Asia WGS AF: 0.362 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10953645; hg19: chr7-109513917;