6-32433440-C-T

Variant names:

• chr6-32433440-C-T
• rs3135338
• ENST00000766007.1:n.280-2709G>A

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-2709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,040 control chromosomes in the GnomAD database, including 30,303 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 0.63 (30303 hom., cov: 33)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 81 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299747	ENST00000766007.1	n.280-2709G>A		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-652C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95063 AN: 151922 Hom.: 30300 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.626 AC: 95107 AN: 152040 Hom.: 30303 Cov.: 33 AF XY: 0.631 AC XY: 46855 AN XY: 74312

African (AFR) AF: 0.487 AC: 20190 AN: 41456

American (AMR) AF: 0.659 AC: 10067 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3466

East Asian (EAS) AF: 0.715 AC: 3699 AN: 5172

South Asian (SAS) AF: 0.698 AC: 3361 AN: 4818

European-Finnish (FIN) AF: 0.705 AC: 7454 AN: 10572

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.674 AC: 45827 AN: 67964

Other (OTH) AF: 0.647 AC: 1367 AN: 2114

Alfa AF: 0.667 Hom.: 127588

Bravo AF: 0.615

Asia WGS AF: 0.675 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.71
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3135338; hg19: chr6-32401217;