13-30032939-T-G

Variant names:

• chr13-30032939-T-G
• rs663528

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 0.571 in 152,038 control chromosomes in the GnomAD database, including 25,133 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 0.57 (25133 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 2 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 = 0.655 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: 0.571 AC: 86722 AN: 151918 Hom.: 25075 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.571 AC: 86850 AN: 152038 Hom.: 25133 Cov.: 33 AF XY: 0.581 AC XY: 43195 AN XY: 74284

African (AFR) AF: 0.623 AC: 25824 AN: 41458

American (AMR) AF: 0.658 AC: 10056 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2101 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3481 AN: 5168

South Asian (SAS) AF: 0.545 AC: 2630 AN: 4828

European-Finnish (FIN) AF: 0.577 AC: 6088 AN: 10552

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34774 AN: 67952

Other (OTH) AF: 0.580 AC: 1225 AN: 2112

Alfa AF: 0.534 Hom.: 67343

Bravo AF: 0.582

Asia WGS AF: 0.622 AC: 2164 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	0.051
DANN	Benign	0.48
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs663528; hg19: chr13-30607076; COSMIC: COSV62998814;