13-68783652-T-C

Variant names:

• chr13-68783652-T-C
• rs1507203

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 0.24 in 151,972 control chromosomes in the GnomAD database, including 4,535 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 (4535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.261 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: 0.240 AC: 36416 AN: 151854 Hom.: 4531 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.240 AC: 36438 AN: 151972 Hom.: 4535 Cov.: 32 AF XY: 0.235 AC XY: 17490 AN XY: 74270

African (AFR) AF: 0.229 AC: 9501 AN: 41496

American (AMR) AF: 0.268 AC: 4080 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3470

East Asian (EAS) AF: 0.0274 AC: 142 AN: 5188

South Asian (SAS) AF: 0.135 AC: 652 AN: 4826

European-Finnish (FIN) AF: 0.247 AC: 2609 AN: 10554

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17699 AN: 67866

Other (OTH) AF: 0.252 AC: 532 AN: 2114

Alfa AF: 0.234 Hom.: 568

Bravo AF: 0.244

Asia WGS AF: 0.104 AC: 359 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.88
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1507203; hg19: chr13-69357784;