rs1123037

Variant names:

• chr4-155593573-T-A
• rs1123037
• ENST00000730967.1:n.*99T>A

Variant summary

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

The ENST00000730967.1(ENSG00000251244):​n.*99T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,912 control chromosomes in the GnomAD database, including 22,032 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 (22032 hom., cov: 31)
• Consequence: ENSG00000251244 ENST00000730967.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 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.*99T>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79726 AN: 151794 Hom.: 22015 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.525 AC: 79802 AN: 151912 Hom.: 22032 Cov.: 31 AF XY: 0.514 AC XY: 38135 AN XY: 74208

African (AFR) AF: 0.700 AC: 29038 AN: 41466

American (AMR) AF: 0.491 AC: 7495 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1819 AN: 3462

East Asian (EAS) AF: 0.256 AC: 1319 AN: 5158

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4814

European-Finnish (FIN) AF: 0.403 AC: 4241 AN: 10514

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

European-Non Finnish (NFE) AF: 0.478 AC: 32500 AN: 67940

Other (OTH) AF: 0.516 AC: 1086 AN: 2106

Alfa AF: 0.505 Hom.: 2478

Bravo AF: 0.541

Asia WGS AF: 0.349 AC: 1213 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.52
DANN	Benign	0.36
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1123037; hg19: chr4-156514725;