rs4331913

Variant names:

• chr5-29246702-C-T
• rs4331913
• ENST00000651494.1:n.172-4714G>A

Variant summary

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

The ENST00000651494.1(ENSG00000286182):​n.172-4714G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,662 control chromosomes in the GnomAD database, including 14,043 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 0.42 (14043 hom., cov: 32)
• Consequence: ENSG00000286182 ENST00000651494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 3 publications found

Genes affected

ENSG00000286182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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
ENSG00000286182	ENST00000651494.1	n.172-4714G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64354 AN: 151544 Hom.: 14043 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.424 AC: 64376 AN: 151662 Hom.: 14043 Cov.: 32 AF XY: 0.421 AC XY: 31205 AN XY: 74102

African (AFR) AF: 0.501 AC: 20737 AN: 41418

American (AMR) AF: 0.404 AC: 6137 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3464

East Asian (EAS) AF: 0.259 AC: 1327 AN: 5126

South Asian (SAS) AF: 0.429 AC: 2065 AN: 4814

European-Finnish (FIN) AF: 0.315 AC: 3315 AN: 10528

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27951 AN: 67798

Other (OTH) AF: 0.457 AC: 967 AN: 2114

Alfa AF: 0.423 Hom.: 33060

Bravo AF: 0.434

Asia WGS AF: 0.389 AC: 1353 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.10
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs4331913; hg19: chr5-29246809;