rs3759504

Variant names:

• chr13-103067909-A-G
• rs3759504

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 0.346 in 152,076 control chromosomes in the GnomAD database, including 9,405 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 0.35 (9405 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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: 0.346 AC: 52640 AN: 151958 Hom.: 9390 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.346 AC: 52690 AN: 152076 Hom.: 9405 Cov.: 33 AF XY: 0.350 AC XY: 26003 AN XY: 74344

African (AFR) AF: 0.374 AC: 15506 AN: 41456

American (AMR) AF: 0.409 AC: 6252 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2116 AN: 5164

South Asian (SAS) AF: 0.331 AC: 1597 AN: 4822

European-Finnish (FIN) AF: 0.353 AC: 3738 AN: 10578

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21394 AN: 67976

Other (OTH) AF: 0.321 AC: 678 AN: 2114

Alfa AF: 0.328 Hom.: 12748

Bravo AF: 0.355

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs3759504; hg19: chr13-103720259;