6-31380039-G-A

Variant names:

• chr6-31380039-G-A
• rs4713462
• ENST00000755446.1:n.327-1941G>A

Variant summary

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

The ENST00000755446.1(ENSG00000298426):​n.327-1941G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,804 control chromosomes in the GnomAD database, including 8,603 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 0.33 (8603 hom., cov: 31)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 25 publications found

Genes affected

ENSG00000298426 (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 = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298426	ENST00000755446.1		n.327-1941G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49546 AN: 151686 Hom.: 8595 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.327 AC: 49586 AN: 151804 Hom.: 8603 Cov.: 31 AF XY: 0.337 AC XY: 24973 AN XY: 74176

African (AFR) AF: 0.277 AC: 11464 AN: 41368

American (AMR) AF: 0.412 AC: 6295 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3466

East Asian (EAS) AF: 0.586 AC: 3018 AN: 5146

South Asian (SAS) AF: 0.461 AC: 2213 AN: 4802

European-Finnish (FIN) AF: 0.371 AC: 3899 AN: 10510

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.292 AC: 19863 AN: 67918

Other (OTH) AF: 0.355 AC: 749 AN: 2110

Alfa AF: 0.316 Hom.: 22352

Bravo AF: 0.327

Asia WGS AF: 0.523 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.82
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4713462; hg19: chr6-31347816;