chr4-155590307-G-T

Variant names:

• chr4-155590307-G-T
• rs1842896
• ENST00000730967.1:n.270-2179G>T

Variant summary

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

The ENST00000730967.1(ENSG00000251244):​n.270-2179G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,740 control chromosomes in the GnomAD database, including 19,782 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 (19782 hom., cov: 33)
• Consequence: ENSG00000251244 ENST00000730967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 31 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.

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
ENSG00000251244	ENST00000730967.1	n.270-2179G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76767 AN: 151622 Hom.: 19778 Cov.: 33

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.506 AC: 76816 AN: 151740 Hom.: 19782 Cov.: 33 AF XY: 0.516 AC XY: 38277 AN XY: 74120

African (AFR) AF: 0.420 AC: 17381 AN: 41386

American (AMR) AF: 0.514 AC: 7831 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1632 AN: 3470

East Asian (EAS) AF: 0.728 AC: 3765 AN: 5170

South Asian (SAS) AF: 0.626 AC: 3009 AN: 4810

European-Finnish (FIN) AF: 0.595 AC: 6252 AN: 10506

Middle Eastern (MID) AF: 0.500 AC: 145 AN: 290

European-Non Finnish (NFE) AF: 0.519 AC: 35220 AN: 67852

Other (OTH) AF: 0.504 AC: 1063 AN: 2110

Alfa AF: 0.513 Hom.: 54813

Bravo AF: 0.494

Asia WGS AF: 0.633 AC: 2191 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.7
DANN	Benign	0.43
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1842896; hg19: chr4-156511459;