chr5-176738085-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000251446 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000251446	ENST00000512245.1	n.63+1311T>C		intron_variant	Intron 1 of 3	4

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

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.508

Alfa AF: 0.527 Hom.: 28889

Bravo AF: 0.529

Asia WGS AF: 0.620 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs490332; hg19: chr5-176165086;