chr10-8536379-C-A

Variant names:

• chr10-8536379-C-A
• rs1830951

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 0.425 in 149,752 control chromosomes in the GnomAD database, including 13,823 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 0.43 (13823 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.49 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: 0.425 AC: 63678 AN: 149676 Hom.: 13825 Cov.: 30

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.425 AC: 63696 AN: 149752 Hom.: 13823 Cov.: 30 AF XY: 0.427 AC XY: 31149 AN XY: 72946

African (AFR) AF: 0.376 AC: 15314 AN: 40766

American (AMR) AF: 0.401 AC: 6030 AN: 15052

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1524 AN: 3454

East Asian (EAS) AF: 0.180 AC: 913 AN: 5086

South Asian (SAS) AF: 0.507 AC: 2410 AN: 4754

European-Finnish (FIN) AF: 0.494 AC: 4881 AN: 9888

Middle Eastern (MID) AF: 0.455 AC: 131 AN: 288

European-Non Finnish (NFE) AF: 0.461 AC: 31134 AN: 67470

Other (OTH) AF: 0.428 AC: 892 AN: 2086

Alfa AF: 0.442 Hom.: 41868

Bravo AF: 0.411

Asia WGS AF: 0.346 AC: 1203 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	0.44
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1830951; hg19: chr10-8578342;