8-42144388-C-T

Variant names:

• chr8-42144388-C-T
• rs13270574
• ENST00000732666.1:n.459-1319G>A

Variant summary

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

The ENST00000732666.1(ENSG00000261449):​n.459-1319G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,800 control chromosomes in the GnomAD database, including 18,596 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 0.49 (18596 hom., cov: 30)
• Consequence: ENSG00000261449 ENST00000732666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 14 publications found

Genes affected

ENSG00000261449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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
ENSG00000261449	ENST00000732666.1	n.459-1319G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73711 AN: 151682 Hom.: 18553 Cov.: 30

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.486 AC: 73819 AN: 151800 Hom.: 18596 Cov.: 30 AF XY: 0.485 AC XY: 35996 AN XY: 74170

African (AFR) AF: 0.618 AC: 25578 AN: 41362

American (AMR) AF: 0.456 AC: 6960 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1846 AN: 3466

East Asian (EAS) AF: 0.479 AC: 2473 AN: 5166

South Asian (SAS) AF: 0.428 AC: 2061 AN: 4812

European-Finnish (FIN) AF: 0.419 AC: 4407 AN: 10524

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28971 AN: 67912

Other (OTH) AF: 0.468 AC: 984 AN: 2104

Alfa AF: 0.456 Hom.: 31782

Bravo AF: 0.495

Asia WGS AF: 0.483 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.96
DANN	Benign	0.39
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs13270574; hg19: chr8-42001906;