rs3918342

Variant names:

• chr13-105533400-C-T
• rs3918342

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 0.466 in 151,914 control chromosomes in the GnomAD database, including 17,059 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 0.47 (17059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 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: 0.466 AC: 70750 AN: 151796 Hom.: 17052 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.466 AC: 70785 AN: 151914 Hom.: 17059 Cov.: 32 AF XY: 0.471 AC XY: 34928 AN XY: 74202

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.452

Alfa AF: 0.491 Hom.: 2975

Bravo AF: 0.458

Asia WGS AF: 0.481 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3918342; hg19: chr13-106185749;