rs947699

Variant names:

• chr10-42998449-C-T
• rs947699

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 0.148 in 152,190 control chromosomes in the GnomAD database, including 1,991 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 0.15 (1991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.148 AC: 22561 AN: 152072 Hom.: 1988 Cov.: 32

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.148 AC: 22588 AN: 152190 Hom.: 1991 Cov.: 32 AF XY: 0.154 AC XY: 11445 AN XY: 74396

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.151

Alfa AF: 0.153 Hom.: 946

Bravo AF: 0.140

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947699; hg19: chr10-43493897;