ENST00000637813.1:n.366-5423A>G

Variant names:

• chr6-43837088-A-G
• rs2396084
• ENST00000637813.1:n.366-5423A>G

Variant summary

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

The ENST00000637813.1(ENSG00000283573):​n.366-5423A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,056 control chromosomes in the GnomAD database, including 29,634 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 0.60 (29634 hom., cov: 31)
• Consequence: ENSG00000283573 ENST00000637813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 10 publications found

Genes affected

ENSG00000283573 (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 (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375069	XR_001744130.1	n.676-77T>C		intron_variant	Intron 2 of 2
LOC105375070	XR_007059588.1	n.193-5423A>G		intron_variant	Intron 1 of 2
LOC105375070	XR_007059589.1	n.193-5423A>G		intron_variant	Intron 1 of 2
LOC105375069	XR_007059590.1	n.393-77T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283573	ENST00000637813.1	n.366-5423A>G		intron_variant	Intron 2 of 2	4
ENSG00000283573	ENST00000719551.1	n.193-5423A>G		intron_variant	Intron 1 of 2
ENSG00000294041	ENST00000720677.1	n.332+114A>G		intron_variant	Intron 1 of 1
ENSG00000294041	ENST00000720678.1	n.325+114A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90962 AN: 151938 Hom.: 29629 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.598 AC: 90998 AN: 152056 Hom.: 29634 Cov.: 31 AF XY: 0.603 AC XY: 44818 AN XY: 74326

African (AFR) AF: 0.316 AC: 13087 AN: 41440

American (AMR) AF: 0.737 AC: 11263 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2498 AN: 3472

East Asian (EAS) AF: 0.801 AC: 4151 AN: 5184

South Asian (SAS) AF: 0.745 AC: 3595 AN: 4826

European-Finnish (FIN) AF: 0.683 AC: 7224 AN: 10576

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47084 AN: 67952

Other (OTH) AF: 0.617 AC: 1305 AN: 2116

Alfa AF: 0.678 Hom.: 27347

Bravo AF: 0.588

Asia WGS AF: 0.730 AC: 2536 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	1.1
DANN	Benign	0.30
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2396084; hg19: chr6-43804825;