13-30089617-T-C

Variant names:

• chr13-30089617-T-C
• rs676495

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 0.623 in 151,954 control chromosomes in the GnomAD database, including 31,067 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 0.62 (31067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.737 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: 0.623 AC: 94650 AN: 151836 Hom.: 31058 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.623 AC: 94680 AN: 151954 Hom.: 31067 Cov.: 31 AF XY: 0.612 AC XY: 45456 AN XY: 74268

African (AFR) AF: 0.486 AC: 20114 AN: 41406

American (AMR) AF: 0.534 AC: 8147 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2840 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1417 AN: 5168

South Asian (SAS) AF: 0.652 AC: 3145 AN: 4824

European-Finnish (FIN) AF: 0.583 AC: 6139 AN: 10538

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50455 AN: 67974

Other (OTH) AF: 0.644 AC: 1358 AN: 2110

Alfa AF: 0.707 Hom.: 16822

Bravo AF: 0.605

Asia WGS AF: 0.431 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs676495; hg19: chr13-30663754;