4-155581296-T-A

Variant names:

• chr4-155581296-T-A
• rs1905262
• ENST00000730967.1:n.270-11190T>A

Variant summary

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

The ENST00000730967.1(ENSG00000251244):​n.270-11190T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,014 control chromosomes in the GnomAD database, including 19,767 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 0.51 (19767 hom., cov: 32)
• Consequence: ENSG00000251244 ENST00000730967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 3 publications found

Genes affected

ENSG00000251244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730967.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251244	ENST00000730967.1		n.270-11190T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76773 AN: 151896 Hom.: 19761 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.505 AC: 76827 AN: 152014 Hom.: 19767 Cov.: 32 AF XY: 0.515 AC XY: 38268 AN XY: 74296

African (AFR) AF: 0.424 AC: 17594 AN: 41488

American (AMR) AF: 0.511 AC: 7790 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1594 AN: 3468

East Asian (EAS) AF: 0.728 AC: 3759 AN: 5162

South Asian (SAS) AF: 0.609 AC: 2933 AN: 4818

European-Finnish (FIN) AF: 0.595 AC: 6275 AN: 10554

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35170 AN: 67956

Other (OTH) AF: 0.499 AC: 1053 AN: 2110

Alfa AF: 0.380 Hom.: 1038

Bravo AF: 0.493

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.87
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs1905262; hg19: chr4-156502448;