rs954108

Variant names:

• chr13-28794569-C-T
• rs954108

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 0.51 in 151,974 control chromosomes in the GnomAD database, including 20,539 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 0.51 (20539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 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: 0.510 AC: 77478 AN: 151856 Hom.: 20534 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.510 AC: 77506 AN: 151974 Hom.: 20539 Cov.: 32 AF XY: 0.504 AC XY: 37416 AN XY: 74280

African (AFR) AF: 0.420 AC: 17385 AN: 41422

American (AMR) AF: 0.479 AC: 7320 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2306 AN: 3468

East Asian (EAS) AF: 0.109 AC: 563 AN: 5164

South Asian (SAS) AF: 0.562 AC: 2701 AN: 4810

European-Finnish (FIN) AF: 0.562 AC: 5922 AN: 10544

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39348 AN: 67972

Other (OTH) AF: 0.535 AC: 1129 AN: 2110

Alfa AF: 0.552 Hom.: 74583

Bravo AF: 0.494

Asia WGS AF: 0.343 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.66
DANN	Benign	0.71
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs954108; hg19: chr13-29368706;