13-68203453-T-C

Variant names:

• chr13-68203453-T-C
• rs6562520

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 0.418 in 152,022 control chromosomes in the GnomAD database, including 14,541 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 0.42 (14541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.417 AC: 63380 AN: 151904 Hom.: 14500 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.418 AC: 63472 AN: 152022 Hom.: 14541 Cov.: 32 AF XY: 0.417 AC XY: 30995 AN XY: 74306

African (AFR) AF: 0.609 AC: 25260 AN: 41446

American (AMR) AF: 0.311 AC: 4756 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2480 AN: 5166

South Asian (SAS) AF: 0.434 AC: 2097 AN: 4830

European-Finnish (FIN) AF: 0.357 AC: 3770 AN: 10554

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22695 AN: 67972

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.367 Hom.: 33692

Bravo AF: 0.424

Asia WGS AF: 0.490 AC: 1703 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.37
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6562520; hg19: chr13-68777585;