6-31380021-G-A

Variant names:

• chr6-31380021-G-A
• rs4713460
• ENST00000755446.1:n.327-1959G>A

Variant summary

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

The ENST00000755446.1(ENSG00000298426):​n.327-1959G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,852 control chromosomes in the GnomAD database, including 8,615 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 (8615 hom., cov: 30)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 18 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298426	ENST00000755446.1		n.327-1959G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49782 AN: 151734 Hom.: 8609 Cov.: 30

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.328 AC: 49820 AN: 151852 Hom.: 8615 Cov.: 30 AF XY: 0.338 AC XY: 25096 AN XY: 74186

African (AFR) AF: 0.280 AC: 11609 AN: 41402

American (AMR) AF: 0.406 AC: 6203 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1791 AN: 3460

East Asian (EAS) AF: 0.570 AC: 2934 AN: 5146

South Asian (SAS) AF: 0.470 AC: 2259 AN: 4802

European-Finnish (FIN) AF: 0.368 AC: 3877 AN: 10526

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20092 AN: 67936

Other (OTH) AF: 0.357 AC: 753 AN: 2110

Alfa AF: 0.316 Hom.: 18404

Bravo AF: 0.327

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.56
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4713460; hg19: chr6-31347798;