rs2346361

Variant names:

• chr5-136112816-G-T
• rs2346361

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 0.463 in 151,980 control chromosomes in the GnomAD database, including 16,613 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 0.46 (16613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70298 AN: 151862 Hom.: 16611 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.463 AC: 70329 AN: 151980 Hom.: 16613 Cov.: 32 AF XY: 0.454 AC XY: 33708 AN XY: 74266

African (AFR) AF: 0.561 AC: 23246 AN: 41454

American (AMR) AF: 0.370 AC: 5657 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1751 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5162

South Asian (SAS) AF: 0.509 AC: 2451 AN: 4812

European-Finnish (FIN) AF: 0.363 AC: 3834 AN: 10556

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30328 AN: 67936

Other (OTH) AF: 0.467 AC: 984 AN: 2108

Alfa AF: 0.451 Hom.: 26246

Bravo AF: 0.466

Asia WGS AF: 0.410 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.41
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2346361; hg19: chr5-135448505;