4-126012137-G-C

Variant names:

• chr4-126012137-G-C
• rs1320267
• ENST00000667497.1:n.164-4180G>C

Variant summary

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

The ENST00000667497.1(ENSG00000250149):​n.164-4180G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,950 control chromosomes in the GnomAD database, including 13,719 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 0.42 (13719 hom., cov: 31)
• Consequence: ENSG00000250149 ENST00000667497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.68
• Publications: 8 publications found

Genes affected

ENSG00000250149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 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
ENSG00000250149	ENST00000667497.1	n.164-4180G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64220 AN: 151832 Hom.: 13710 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.423 AC: 64269 AN: 151950 Hom.: 13719 Cov.: 31 AF XY: 0.424 AC XY: 31495 AN XY: 74262

African (AFR) AF: 0.370 AC: 15314 AN: 41428

American (AMR) AF: 0.513 AC: 7827 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3464

East Asian (EAS) AF: 0.371 AC: 1909 AN: 5152

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4782 AN: 10568

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.431 AC: 29288 AN: 67950

Other (OTH) AF: 0.426 AC: 899 AN: 2112

Alfa AF: 0.276 Hom.: 677

Bravo AF: 0.424

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.066
DANN	Benign	0.37
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs1320267; hg19: chr4-126933292;