13-113105441-G-T

Variant names:

• chr13-113105441-G-T
• rs510335

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 0.175 in 152,122 control chromosomes in the GnomAD database, including 2,918 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 0.17 (2918 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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: 0.175 AC: 26564 AN: 152004 Hom.: 2911 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.175 AC: 26604 AN: 152122 Hom.: 2918 Cov.: 31 AF XY: 0.174 AC XY: 12946 AN XY: 74372

African (AFR) AF: 0.303 AC: 12536 AN: 41438

American (AMR) AF: 0.143 AC: 2184 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3466

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5184

South Asian (SAS) AF: 0.273 AC: 1312 AN: 4812

European-Finnish (FIN) AF: 0.0756 AC: 802 AN: 10602

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8284 AN: 68014

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.152 Hom.: 488

Bravo AF: 0.183

Asia WGS AF: 0.165 AC: 573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.094
PhyloP100		-0.30
PromoterAI		0.29	Neutral

Splicing

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

Other links and lift over

dbSNP: rs510335; hg19: chr13-113759755;