rs957646

chr10-90304565-T-C

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 0.0937 in 152,162 control chromosomes in the GnomAD database, including 1,212 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 0.094 (1212 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.0938 AC: 14256 AN: 152044 Hom.: 1212 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0937 AC: 14260 AN: 152162 Hom.: 1212 Cov.: 32 AF XY: 0.0903 AC XY: 6717 AN XY: 74404

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.0270

Gnomad4 NFE AF: 0.0450

Gnomad4 OTH AF: 0.0744

Alfa AF: 0.0656 Hom.: 106

Bravo AF: 0.103

Asia WGS AF: 0.0250 AC: 90 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957646; hg19: chr10-92064322;