rs11594687

Variant names:

• chr10-95578774-C-T
• rs11594687

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 0.0787 in 152,256 control chromosomes in the GnomAD database, including 555 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 0.079 (555 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.0993 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: 0.0788 AC: 11983 AN: 152138 Hom.: 553 Cov.: 31

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0899

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

GnomAD4 genome AF: 0.0787 AC: 11982 AN: 152256 Hom.: 555 Cov.: 31 AF XY: 0.0792 AC XY: 5895 AN XY: 74452

African (AFR) AF: 0.0383 AC: 1591 AN: 41560

American (AMR) AF: 0.0790 AC: 1209 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5184

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1370 AN: 10590

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

European-Non Finnish (NFE) AF: 0.101 AC: 6887 AN: 68002

Other (OTH) AF: 0.0894 AC: 189 AN: 2114

Alfa AF: 0.0943 Hom.: 161

Bravo AF: 0.0742

Asia WGS AF: 0.0210 AC: 74 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	1.7
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11594687; hg19: chr10-97338531;