4-38952600-T-C

Variant names:

• chr4-38952600-T-C
• rs10021255
• ENST00000752065.1:n.*101A>G

Variant summary

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

The ENST00000752065.1(ENSG00000297959):​n.*101A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,098 control chromosomes in the GnomAD database, including 35,795 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 0.68 (35795 hom., cov: 32)
• Consequence: ENSG00000297959 ENST00000752065.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 2 publications found

Genes affected

ENSG00000297959 (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 (AFR) allele frequency at 95% confidence interval = 0.841 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
ENSG00000297959	ENST00000752065.1	n.*101A>G		downstream_gene_variant
ENSG00000297959	ENST00000752066.1	n.*114A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102741 AN: 151980 Hom.: 35716 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.676 AC: 102886 AN: 152098 Hom.: 35795 Cov.: 32 AF XY: 0.675 AC XY: 50176 AN XY: 74332

African (AFR) AF: 0.848 AC: 35199 AN: 41506

American (AMR) AF: 0.632 AC: 9659 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3472

East Asian (EAS) AF: 0.665 AC: 3443 AN: 5174

South Asian (SAS) AF: 0.730 AC: 3524 AN: 4830

European-Finnish (FIN) AF: 0.566 AC: 5968 AN: 10550

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41025 AN: 67968

Other (OTH) AF: 0.669 AC: 1411 AN: 2108

Alfa AF: 0.670 Hom.: 4484

Bravo AF: 0.685

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.56
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs10021255; hg19: chr4-38954221;