chr13-30764963-T-G

Variant names:

• chr13-30764963-T-G
• rs9315053

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 0.244 in 152,232 control chromosomes in the GnomAD database, including 5,727 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 0.24 (5727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.322 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: 0.244 AC: 37111 AN: 152114 Hom.: 5726 Cov.: 33

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.244 AC: 37119 AN: 152232 Hom.: 5727 Cov.: 33 AF XY: 0.246 AC XY: 18321 AN XY: 74408

African (AFR) AF: 0.0581 AC: 2415 AN: 41574

American (AMR) AF: 0.330 AC: 5043 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1306 AN: 5176

South Asian (SAS) AF: 0.247 AC: 1193 AN: 4826

European-Finnish (FIN) AF: 0.341 AC: 3607 AN: 10580

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21831 AN: 68004

Other (OTH) AF: 0.240 AC: 507 AN: 2114

Alfa AF: 0.274 Hom.: 944

Bravo AF: 0.237

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs9315053; hg19: chr13-31339100;