rs3918342

Positions:

• chr13-105533400-C-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 0.466 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;