rs3759503

chr13-103068072-G-Achr13-103068072-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;