4-62787417-G-T

Variant names:

• chr4-62787417-G-T
• rs7441398
• ENST00000751407.1:n.159-2794G>T

Variant summary

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

The ENST00000751407.1(ENSG00000297853):​n.159-2794G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,994 control chromosomes in the GnomAD database, including 9,085 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 0.29 (9085 hom., cov: 32)
• Consequence: ENSG00000297853 ENST00000751407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 5 publications found

Genes affected

ENSG00000297853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 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
ENSG00000297853	ENST00000751407.1	n.159-2794G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43555 AN: 151876 Hom.: 9051 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0791

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.287 AC: 43646 AN: 151994 Hom.: 9085 Cov.: 32 AF XY: 0.289 AC XY: 21486 AN XY: 74280

African (AFR) AF: 0.544 AC: 22540 AN: 41456

American (AMR) AF: 0.199 AC: 3041 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0791 AC: 274 AN: 3462

East Asian (EAS) AF: 0.712 AC: 3669 AN: 5156

South Asian (SAS) AF: 0.337 AC: 1627 AN: 4828

European-Finnish (FIN) AF: 0.167 AC: 1759 AN: 10548

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10041 AN: 67966

Other (OTH) AF: 0.243 AC: 515 AN: 2116

Alfa AF: 0.187 Hom.: 11522

Bravo AF: 0.298

Asia WGS AF: 0.541 AC: 1873 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs7441398; hg19: chr4-63653135;