rs152341

Variant names:

• chr5-60550136-T-A
• rs152341

Your query was ambiguous. Multiple possible variants found:

• chr5-60550136-T-A
• chr5-60550136-T-C
• chr5-60550136-T-G

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 0.451 in 151,966 control chromosomes in the GnomAD database, including 16,698 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 0.45 (16698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 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: 0.451 AC: 68549 AN: 151848 Hom.: 16695 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.451 AC: 68553 AN: 151966 Hom.: 16698 Cov.: 32 AF XY: 0.449 AC XY: 33321 AN XY: 74262

African (AFR) AF: 0.258 AC: 10700 AN: 41480

American (AMR) AF: 0.548 AC: 8363 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1886 AN: 3464

East Asian (EAS) AF: 0.563 AC: 2910 AN: 5166

South Asian (SAS) AF: 0.313 AC: 1504 AN: 4804

European-Finnish (FIN) AF: 0.492 AC: 5189 AN: 10556

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36334 AN: 67918

Other (OTH) AF: 0.467 AC: 985 AN: 2108

Alfa AF: 0.488 Hom.: 2335

Bravo AF: 0.451

Asia WGS AF: 0.427 AC: 1487 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.091
DANN	Benign	0.21
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs152341; hg19: chr5-59845963;