ENST00000734076.1:n.299-64578C>A

Variant names:

• chr4-4032235-G-T
• rs10937624
• ENST00000734076.1:n.299-64578C>A

Variant summary

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

The ENST00000734076.1(ENSG00000290888):​n.299-64578C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,842 control chromosomes in the GnomAD database, including 25,797 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 0.58 (25797 hom., cov: 32)
• Consequence: ENSG00000290888 ENST00000734076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 2 publications found

Genes affected

ENSG00000290888 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928217	XR_001741557.2	n.58+474G>T		intron_variant	Intron 1 of 2
LOC101928217	XR_001741554.2	n.-182G>T		upstream_gene_variant
LOC101928217	XR_001741555.2	n.-186G>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290888	ENST00000734076.1	n.299-64578C>A		intron_variant	Intron 1 of 2
ENSG00000290888	ENST00000734080.1	n.298-2941C>A		intron_variant	Intron 1 of 1
ENSG00000290888	ENST00000734091.1	n.409-2941C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87728 AN: 151722 Hom.: 25779 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.578 AC: 87789 AN: 151842 Hom.: 25797 Cov.: 32 AF XY: 0.582 AC XY: 43192 AN XY: 74218

African (AFR) AF: 0.588 AC: 24321 AN: 41342

American (AMR) AF: 0.600 AC: 9149 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1951 AN: 3464

East Asian (EAS) AF: 0.724 AC: 3742 AN: 5170

South Asian (SAS) AF: 0.768 AC: 3704 AN: 4822

European-Finnish (FIN) AF: 0.546 AC: 5773 AN: 10566

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37306 AN: 67910

Other (OTH) AF: 0.592 AC: 1248 AN: 2108

Alfa AF: 0.563 Hom.: 3060

Bravo AF: 0.580

Asia WGS AF: 0.708 AC: 2459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10937624; hg19: chr4-4033962;