13-105516850-C-T

Variant names:

• chr13-105516850-C-T
• rs778293

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 0.535 in 151,894 control chromosomes in the GnomAD database, including 23,019 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 0.54 (23019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.717 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: 0.535 AC: 81225 AN: 151776 Hom.: 22998 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.535 AC: 81286 AN: 151894 Hom.: 23019 Cov.: 32 AF XY: 0.540 AC XY: 40046 AN XY: 74226

African (AFR) AF: 0.337 AC: 13956 AN: 41420

American (AMR) AF: 0.597 AC: 9106 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3617 AN: 5172

South Asian (SAS) AF: 0.737 AC: 3550 AN: 4814

European-Finnish (FIN) AF: 0.581 AC: 6112 AN: 10516

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.607 AC: 41247 AN: 67920

Other (OTH) AF: 0.528 AC: 1116 AN: 2112

Alfa AF: 0.578 Hom.: 48064

Bravo AF: 0.523

Asia WGS AF: 0.647 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.45
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs778293; hg19: chr13-106169199;