5-40410833-G-T

Variant names:

• chr5-40410833-G-T
• rs6451493
• ENST00000809861.1:n.239-230C>A

Variant summary

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

The ENST00000809861.1(ENSG00000305258):​n.239-230C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,900 control chromosomes in the GnomAD database, including 25,485 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 0.57 (25485 hom., cov: 32)
• Consequence: ENSG00000305258 ENST00000809861.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 37 publications found

Genes affected

ENSG00000305258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 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
ENSG00000305258	ENST00000809861.1	n.239-230C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86694 AN: 151782 Hom.: 25470 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.571 AC: 86753 AN: 151900 Hom.: 25485 Cov.: 32 AF XY: 0.564 AC XY: 41844 AN XY: 74234

African (AFR) AF: 0.613 AC: 25354 AN: 41392

American (AMR) AF: 0.475 AC: 7252 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3468

East Asian (EAS) AF: 0.143 AC: 739 AN: 5162

South Asian (SAS) AF: 0.471 AC: 2269 AN: 4816

European-Finnish (FIN) AF: 0.545 AC: 5746 AN: 10536

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41167 AN: 67942

Other (OTH) AF: 0.584 AC: 1229 AN: 2106

Alfa AF: 0.581 Hom.: 78745

Bravo AF: 0.564

Asia WGS AF: 0.373 AC: 1297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs6451493; hg19: chr5-40410935;