chr4-137832570-T-C

Variant names:

• chr4-137832570-T-C
• rs1509269
• ENST00000765862.1:n.216-18169A>G

Variant summary

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

The ENST00000765862.1(ENSG00000250126):​n.216-18169A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,200 control chromosomes in the GnomAD database, including 60,840 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 0.89 (60840 hom., cov: 32)
• Consequence: ENSG00000250126 ENST00000765862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463
• Publications: 3 publications found

Genes affected

ENSG00000250126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.926 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
ENSG00000250126	ENST00000765862.1	n.216-18169A>G		intron_variant	Intron 1 of 4
ENSG00000250126	ENST00000765863.1	n.216-18169A>G		intron_variant	Intron 1 of 3
ENSG00000250126	ENST00000765866.1	n.231-18169A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135882 AN: 152082 Hom.: 60787 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.894 AC: 135994 AN: 152200 Hom.: 60840 Cov.: 32 AF XY: 0.893 AC XY: 66416 AN XY: 74410

African (AFR) AF: 0.872 AC: 36218 AN: 41532

American (AMR) AF: 0.938 AC: 14346 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3226 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4870 AN: 5162

South Asian (SAS) AF: 0.949 AC: 4573 AN: 4818

European-Finnish (FIN) AF: 0.852 AC: 9012 AN: 10580

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60648 AN: 68026

Other (OTH) AF: 0.913 AC: 1931 AN: 2114

Alfa AF: 0.897 Hom.: 24846

Bravo AF: 0.899

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.35
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1509269; hg19: chr4-138753724;