3-35500-A-G

Variant names:

• chr3-35500-A-G
• rs1400174

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 0.281 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.170 AC: 7040 AN: 41294

American (AMR) AF: 0.339 AC: 5163 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3466

East Asian (EAS) AF: 0.537 AC: 2763 AN: 5146

South Asian (SAS) AF: 0.246 AC: 1183 AN: 4806

European-Finnish (FIN) AF: 0.377 AC: 3944 AN: 10468

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.311 AC: 21101 AN: 67904

Other (OTH) AF: 0.278 AC: 584 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.61
DANN	Benign	0.41
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1400174; hg19: chr3-77174;