6-31353346-G-T

Variant names:

• chr6-31353346-G-T
• rs2523612
• ENST00000755297.1:n.33-2855G>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-2855G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 151,658 control chromosomes in the GnomAD database, including 59,585 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 0.89 (59585 hom., cov: 28)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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.33-2855G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134216 AN: 151540 Hom.: 59525 Cov.: 28

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.886 AC: 134333 AN: 151658 Hom.: 59585 Cov.: 28 AF XY: 0.889 AC XY: 65898 AN XY: 74098

African (AFR) AF: 0.890 AC: 36670 AN: 41200

American (AMR) AF: 0.922 AC: 14069 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3395 AN: 3466

East Asian (EAS) AF: 0.983 AC: 5063 AN: 5148

South Asian (SAS) AF: 0.963 AC: 4638 AN: 4814

European-Finnish (FIN) AF: 0.869 AC: 9168 AN: 10544

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58281 AN: 67930

Other (OTH) AF: 0.917 AC: 1921 AN: 2096

Alfa AF: 0.867 Hom.: 35342

Bravo AF: 0.891

Asia WGS AF: 0.961 AC: 3343 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	0.18
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2523612; hg19: chr6-31321123;