rs1400174

chr3-35500-A-Gchr3-35500-A-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 0.281 in 151,608 control chromosomes in the GnomAD database, including 6,660 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 0.28 (6660 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 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: 0.281 AC: 42619 AN: 151490 Hom.: 6655 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.281 AC: 42651 AN: 151608 Hom.: 6660 Cov.: 31 AF XY: 0.285 AC XY: 21131 AN XY: 74046

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.278

Alfa AF: 0.297 Hom.: 985

Bravo AF: 0.274

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.61
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1400174; hg19: chr3-77174;