13-108205682-T-C

Variant names:

• chr13-108205682-T-C
• rs1151402

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 0.651 in 152,026 control chromosomes in the GnomAD database, including 33,536 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 0.65 (33536 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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: 0.651 AC: 98850 AN: 151908 Hom.: 33473 Cov.: 31

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.651 AC: 98978 AN: 152026 Hom.: 33536 Cov.: 31 AF XY: 0.651 AC XY: 48335 AN XY: 74296

African (AFR) AF: 0.811 AC: 33661 AN: 41490

American (AMR) AF: 0.699 AC: 10678 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1948 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2142 AN: 5152

South Asian (SAS) AF: 0.354 AC: 1705 AN: 4818

European-Finnish (FIN) AF: 0.736 AC: 7780 AN: 10570

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39051 AN: 67940

Other (OTH) AF: 0.623 AC: 1316 AN: 2114

Alfa AF: 0.616 Hom.: 10370

Bravo AF: 0.662

Asia WGS AF: 0.449 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1151402; hg19: chr13-108858030;