9-31077303-C-T

Variant names:

• chr9-31077303-C-T
• rs10511874

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 0.0517 in 151,566 control chromosomes in the GnomAD database, including 363 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 0.052 (363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.0518 AC: 7844 AN: 151450 Hom.: 364 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.0291

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0437

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

GnomAD4 genome AF: 0.0517 AC: 7843 AN: 151566 Hom.: 363 Cov.: 32 AF XY: 0.0548 AC XY: 4060 AN XY: 74084

African (AFR) AF: 0.0629 AC: 2604 AN: 41418

American (AMR) AF: 0.0560 AC: 849 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3460

East Asian (EAS) AF: 0.250 AC: 1288 AN: 5148

South Asian (SAS) AF: 0.0293 AC: 141 AN: 4806

European-Finnish (FIN) AF: 0.0770 AC: 814 AN: 10572

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0294 AC: 1993 AN: 67680

Other (OTH) AF: 0.0442 AC: 93 AN: 2104

Alfa AF: 0.0116 Hom.: 2

Bravo AF: 0.0560

Asia WGS AF: 0.128 AC: 443 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.60
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs10511874; hg19: chr9-31077301;