4-1045427-A-G

Variant names:

• chr4-1045427-A-G
• rs62296075
• ENST00000721865.1:n.120-5788A>G

Variant summary

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

The ENST00000721865.1(ENSG00000294205):​n.120-5788A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,322 control chromosomes in the GnomAD database, including 235 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 0.051 (235 hom., cov: 33)
• Consequence: ENSG00000294205 ENST00000721865.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 5 publications found

Genes affected

ENSG00000294205 (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 (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374343	XR_001741546.1	n.2077-5788A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294205	ENST00000721865.1	n.120-5788A>G		intron_variant	Intron 1 of 1
ENSG00000294205	ENST00000721866.1	n.338-5788A>G		intron_variant	Intron 1 of 1
ENSG00000294205	ENST00000721867.1	n.137-5788A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7734 AN: 152204 Hom.: 234 Cov.: 33

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0509 AC: 7751 AN: 152322 Hom.: 235 Cov.: 33 AF XY: 0.0497 AC XY: 3700 AN XY: 74488

African (AFR) AF: 0.0332 AC: 1379 AN: 41586

American (AMR) AF: 0.0436 AC: 668 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.0772 AC: 268 AN: 3470

East Asian (EAS) AF: 0.139 AC: 718 AN: 5166

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4834

European-Finnish (FIN) AF: 0.0487 AC: 517 AN: 10622

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0575 AC: 3913 AN: 68012

Other (OTH) AF: 0.0743 AC: 157 AN: 2112

Alfa AF: 0.0345 Hom.: 26

Bravo AF: 0.0514

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs62296075; hg19: chr4-1039215;