rs3759503

Variant names:

• chr13-103068072-G-A
• rs3759503

Your query was ambiguous. Multiple possible variants found:

• chr13-103068072-G-A
• chr13-103068072-G-C
• chr13-103068072-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.343 in 152,124 control chromosomes in the GnomAD database, including 9,246 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 0.34 (9246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) 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: 0.343 AC: 52184 AN: 152006 Hom.: 9232 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.343 AC: 52232 AN: 152124 Hom.: 9246 Cov.: 32 AF XY: 0.347 AC XY: 25817 AN XY: 74404

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.318

Alfa AF: 0.204 Hom.: 425

Bravo AF: 0.351

Asia WGS AF: 0.320 AC: 1115 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	1.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3759503; hg19: chr13-103720422;