6-31274397-G-A

Variant names:

• chr6-31274397-G-A
• rs2524079
• ENST00000755297.1:n.32+3291G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+3291G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 149,986 control chromosomes in the GnomAD database, including 15,074 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 0.44 (15074 hom., cov: 25)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 19 publications found

Genes affected

ENSG00000298396 (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 (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.32+3291G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 66276 AN: 149870 Hom.: 15067 Cov.: 25

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.442 AC: 66320 AN: 149986 Hom.: 15074 Cov.: 25 AF XY: 0.441 AC XY: 32265 AN XY: 73088

African (AFR) AF: 0.440 AC: 17856 AN: 40548

American (AMR) AF: 0.452 AC: 6836 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2574 AN: 3462

East Asian (EAS) AF: 0.290 AC: 1476 AN: 5098

South Asian (SAS) AF: 0.485 AC: 2296 AN: 4730

European-Finnish (FIN) AF: 0.410 AC: 4133 AN: 10082

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29473 AN: 67658

Other (OTH) AF: 0.480 AC: 996 AN: 2074

Alfa AF: 0.272 Hom.: 571

Bravo AF: 0.443

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.16
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2524079; hg19: chr6-31242174;