rs2346361

Variant names:

• chr5-136112816-G-T
• rs2346361

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 0.463 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.463 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

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.467

Alfa AF: 0.448 Hom.: 20586

Bravo AF: 0.466

Asia WGS AF: 0.410 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
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: rs2346361; hg19: chr5-135448505;