6-32417622-A-G

Variant names:

• chr6-32417622-A-G
• rs3135377
• ENST00000766247.1:n.282+3252A>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+3252A>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 152,208 control chromosomes in the GnomAD database, including 49,538 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 0.80 (49538 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 23 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299769	ENST00000766247.1		n.282+3252A>G		intron	N/A
	ENSG00000299769	ENST00000766248.1		n.286+3252A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122372 AN: 152090 Hom.: 49506 Cov.: 32

Gnomad AFR AF: 0.769

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: 0.879

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.805 AC: 122456 AN: 152208 Hom.: 49538 Cov.: 32 AF XY: 0.810 AC XY: 60298 AN XY: 74430

African (AFR) AF: 0.769 AC: 31901 AN: 41502

American (AMR) AF: 0.817 AC: 12498 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3122 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5060 AN: 5184

South Asian (SAS) AF: 0.927 AC: 4479 AN: 4830

European-Finnish (FIN) AF: 0.859 AC: 9107 AN: 10604

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.787 AC: 53535 AN: 68000

Other (OTH) AF: 0.810 AC: 1711 AN: 2112

Alfa AF: 0.796 Hom.: 42389

Bravo AF: 0.797

Asia WGS AF: 0.923 AC: 3205 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	1.9
DANN	Benign	0.57
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs3135377; hg19: chr6-32385399;