rs27342

Variant names:

• chr5-112129735-T-C
• rs27342

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 0.36 in 151,988 control chromosomes in the GnomAD database, including 11,686 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 0.36 (11686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.360 AC: 54606 AN: 151870 Hom.: 11663 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.360 AC: 54689 AN: 151988 Hom.: 11686 Cov.: 32 AF XY: 0.358 AC XY: 26601 AN XY: 74290

African (AFR) AF: 0.604 AC: 25022 AN: 41428

American (AMR) AF: 0.325 AC: 4960 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.159 AC: 824 AN: 5170

South Asian (SAS) AF: 0.238 AC: 1142 AN: 4808

European-Finnish (FIN) AF: 0.259 AC: 2735 AN: 10566

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18282 AN: 67976

Other (OTH) AF: 0.316 AC: 666 AN: 2108

Alfa AF: 0.302 Hom.: 7995

Bravo AF: 0.374

Asia WGS AF: 0.287 AC: 997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.84
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs27342; hg19: chr5-111465432;