6-32415273-A-G

Variant names:

• chr6-32415273-A-G
• rs4959027
• ENST00000766247.1:n.282+903A>G

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,014 control chromosomes in the GnomAD database, including 49,574 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 0.81 (49574 hom., cov: 29)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 17 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766247.1. 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
	ENSG00000299769	ENST00000766247.1		n.282+903A>G		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.286+903A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122340 AN: 151896 Hom.: 49539 Cov.: 29

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.805 AC: 122428 AN: 152014 Hom.: 49574 Cov.: 29 AF XY: 0.811 AC XY: 60272 AN XY: 74304

African (AFR) AF: 0.772 AC: 31960 AN: 41414

American (AMR) AF: 0.817 AC: 12481 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3121 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5040 AN: 5164

South Asian (SAS) AF: 0.927 AC: 4468 AN: 4818

European-Finnish (FIN) AF: 0.859 AC: 9080 AN: 10574

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53522 AN: 67980

Other (OTH) AF: 0.811 AC: 1712 AN: 2110

Alfa AF: 0.806 Hom.: 106847

Bravo AF: 0.798

Asia WGS AF: 0.923 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.40
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4959027; hg19: chr6-32383050;