rs952382

Variant names:

• chr5-54931776-C-A
• rs952382
• ENST00000736670.1:n.371+12254G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000736670.1(ENSG00000296132):​n.371+12254G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000296132 ENST00000736670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 5 publications found

Genes affected

ENSG00000296132 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736670.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296132	ENST00000736670.1		n.371+12254G>T		intron	N/A

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

African (AFR) AF: 0.0717 AC: 2978 AN: 41538

American (AMR) AF: 0.243 AC: 3713 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2480 AN: 5168

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4812

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10578

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14188 AN: 67990

Other (OTH) AF: 0.205 AC: 432 AN: 2106

Alfa AF: 0.198 Hom.: 8984

Bravo AF: 0.182

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs952382;

hg19: chr5-54227604;

COSMIC: COSV60133379;