5-176738085-A-G

Variant names:

• chr5-176738085-A-G
• rs490332
• ENST00000512245.1:n.63+1311T>C

Variant summary

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

The ENST00000512245.1(ENSG00000251446):​n.63+1311T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,044 control chromosomes in the GnomAD database, including 21,226 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 0.53 (21226 hom., cov: 33)
• Consequence: ENSG00000251446 ENST00000512245.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 6 publications found

Genes affected

ENSG00000251446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512245.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251446	ENST00000512245.1	TSL:4	n.63+1311T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80149 AN: 151926 Hom.: 21206 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.528 AC: 80217 AN: 152044 Hom.: 21226 Cov.: 33 AF XY: 0.529 AC XY: 39310 AN XY: 74308

African (AFR) AF: 0.506 AC: 20986 AN: 41474

American (AMR) AF: 0.552 AC: 8438 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1747 AN: 3468

East Asian (EAS) AF: 0.642 AC: 3310 AN: 5152

South Asian (SAS) AF: 0.568 AC: 2732 AN: 4812

European-Finnish (FIN) AF: 0.540 AC: 5706 AN: 10560

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35649 AN: 67974

Other (OTH) AF: 0.508 AC: 1072 AN: 2110

Alfa AF: 0.531 Hom.: 69147

Bravo AF: 0.529

Asia WGS AF: 0.620 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs490332; hg19: chr5-176165086;