rs10819510

Variant names:

• chr9-129393385-A-G
• rs10819510

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 0.517 in 152,014 control chromosomes in the GnomAD database, including 22,385 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 0.52 (22385 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 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: 0.517 AC: 78505 AN: 151894 Hom.: 22383 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.517 AC: 78521 AN: 152014 Hom.: 22385 Cov.: 33 AF XY: 0.519 AC XY: 38541 AN XY: 74296

African (AFR) AF: 0.258 AC: 10688 AN: 41454

American (AMR) AF: 0.575 AC: 8786 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1987 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3386 AN: 5142

South Asian (SAS) AF: 0.439 AC: 2117 AN: 4822

European-Finnish (FIN) AF: 0.679 AC: 7173 AN: 10564

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42411 AN: 67968

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.592 Hom.: 39127

Bravo AF: 0.502

Asia WGS AF: 0.499 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.048
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10819510; hg19: chr9-132155664;