rs10513414

Variant names:

• chr9-122843429-T-C
• rs10513414

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 0.0828 in 152,032 control chromosomes in the GnomAD database, including 1,654 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 0.083 (1654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 6 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 = 0.584 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: 0.0826 AC: 12553 AN: 151928 Hom.: 1641 Cov.: 32

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0828 AC: 12587 AN: 152032 Hom.: 1654 Cov.: 32 AF XY: 0.0900 AC XY: 6685 AN XY: 74282

African (AFR) AF: 0.0301 AC: 1249 AN: 41496

American (AMR) AF: 0.233 AC: 3556 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.602 AC: 3094 AN: 5140

South Asian (SAS) AF: 0.105 AC: 505 AN: 4810

European-Finnish (FIN) AF: 0.0671 AC: 708 AN: 10544

Middle Eastern (MID) AF: 0.0342 AC: 10 AN: 292

European-Non Finnish (NFE) AF: 0.0436 AC: 2964 AN: 67984

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.0649 Hom.: 1663

Bravo AF: 0.0995

Asia WGS AF: 0.335 AC: 1159 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	0.12
DANN	Benign	0.28
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10513414; hg19: chr9-125605708;