rs10948693

Variant names:

• chr6-52289201-G-A
• rs10948693

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0892 in 152,134 control chromosomes in the GnomAD database, including 752 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 0.089 (752 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.131 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: 0.0893 AC: 13572 AN: 152014 Hom.: 751 Cov.: 33

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0892 AC: 13569 AN: 152134 Hom.: 752 Cov.: 33 AF XY: 0.0886 AC XY: 6588 AN XY: 74382

African (AFR) AF: 0.0259 AC: 1076 AN: 41536

American (AMR) AF: 0.0866 AC: 1324 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3470

East Asian (EAS) AF: 0.139 AC: 720 AN: 5174

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4816

European-Finnish (FIN) AF: 0.0772 AC: 815 AN: 10562

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8089 AN: 67978

Other (OTH) AF: 0.110 AC: 231 AN: 2108

Alfa AF: 0.111 Hom.: 1055

Bravo AF: 0.0874

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.52
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs10948693; hg19: chr6-52153999;