rs952382

Variant names:

• chr5-54931776-C-A
• rs952382

Your query was ambiguous. Multiple possible variants found:

• chr5-54931776-C-A
• chr5-54931776-C-T

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 0.192 in 152,142 control chromosomes in the GnomAD database, including 3,486 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 0.19 (3486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 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: 0.192 AC: 29236 AN: 152024 Hom.: 3488 Cov.: 32

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.192 AC: 29229 AN: 152142 Hom.: 3486 Cov.: 32 AF XY: 0.200 AC XY: 14890 AN XY: 74368

Gnomad4 AFR AF: 0.0717

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.205

Alfa AF: 0.204 Hom.: 5451

Bravo AF: 0.182

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952382; hg19: chr5-54227604; COSMIC: COSV60133379;