6-31353033-A-G

Variant names:

• chr6-31353033-A-G
• rs2596503
• ENST00000755297.1:n.33-3168A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.33-3168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,108 control chromosomes in the GnomAD database, including 53,574 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 0.84 (53574 hom., cov: 31)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 44 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.892 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.33-3168A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127262 AN: 151990 Hom.: 53512 Cov.: 31

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.837 AC: 127383 AN: 152108 Hom.: 53574 Cov.: 31 AF XY: 0.841 AC XY: 62544 AN XY: 74376

African (AFR) AF: 0.853 AC: 35398 AN: 41478

American (AMR) AF: 0.905 AC: 13843 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3306 AN: 3472

East Asian (EAS) AF: 0.836 AC: 4324 AN: 5172

South Asian (SAS) AF: 0.873 AC: 4212 AN: 4826

European-Finnish (FIN) AF: 0.812 AC: 8584 AN: 10574

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54756 AN: 67968

Other (OTH) AF: 0.888 AC: 1877 AN: 2114

Alfa AF: 0.827 Hom.: 208149

Bravo AF: 0.847

Asia WGS AF: 0.867 AC: 3018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.2
DANN	Benign	0.45
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2596503; hg19: chr6-31320810;