rs10509977

Variant names:

• chr10-113434040-G-A
• rs10509977

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 0.169 in 152,174 control chromosomes in the GnomAD database, including 2,705 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 0.17 (2705 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.169 AC: 25679 AN: 152056 Hom.: 2710 Cov.: 33

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.169 AC: 25663 AN: 152174 Hom.: 2705 Cov.: 33 AF XY: 0.166 AC XY: 12380 AN XY: 74386

African (AFR) AF: 0.0466 AC: 1935 AN: 41528

American (AMR) AF: 0.177 AC: 2703 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1060 AN: 5178

South Asian (SAS) AF: 0.133 AC: 641 AN: 4822

European-Finnish (FIN) AF: 0.174 AC: 1836 AN: 10574

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15718 AN: 68002

Other (OTH) AF: 0.213 AC: 448 AN: 2108

Alfa AF: 0.186 Hom.: 483

Bravo AF: 0.164

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10509977; hg19: chr10-115193799;