rs10830964

Variant names:

• chr11-92986515-C-T
• rs10830964

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 0.135 in 152,174 control chromosomes in the GnomAD database, including 1,985 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 0.14 (1985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 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: 0.135 AC: 20574 AN: 152056 Hom.: 1975 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.135 AC: 20599 AN: 152174 Hom.: 1985 Cov.: 32 AF XY: 0.144 AC XY: 10698 AN XY: 74386

African (AFR) AF: 0.0307 AC: 1274 AN: 41524

American (AMR) AF: 0.323 AC: 4942 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1153 AN: 5174

South Asian (SAS) AF: 0.191 AC: 924 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9227 AN: 67996

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.0909 Hom.: 498

Bravo AF: 0.143

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.70
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10830964; hg19: chr11-92719681;