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. The variant received -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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.364 AC: 15091 AN: 41482

American (AMR) AF: 0.409 AC: 6247 AN: 15282

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

East Asian (EAS) AF: 0.395 AC: 2045 AN: 5178

South Asian (SAS) AF: 0.335 AC: 1616 AN: 4826

European-Finnish (FIN) AF: 0.353 AC: 3744 AN: 10594

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

European-Non Finnish (NFE) AF: 0.315 AC: 21407 AN: 67974

Other (OTH) AF: 0.318 AC: 672 AN: 2110

Alfa AF: 0.303 Hom.: 2036

Bravo AF: 0.351

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs3759503; hg19: chr13-103720422;