rs3135335

Variant names:

• chr6-32434068-C-G
• rs3135335
• ENST00000766007.1:n.280-3337G>C

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-3337G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,990 control chromosomes in the GnomAD database, including 30,273 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 (30273 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 24 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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.280-3337G>C		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-24C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95003 AN: 151872 Hom.: 30270 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.737

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: 0.625 AC: 95047 AN: 151990 Hom.: 30273 Cov.: 32 AF XY: 0.630 AC XY: 46821 AN XY: 74296

African (AFR) AF: 0.487 AC: 20163 AN: 41430

American (AMR) AF: 0.659 AC: 10072 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2315 AN: 3466

East Asian (EAS) AF: 0.714 AC: 3694 AN: 5174

South Asian (SAS) AF: 0.698 AC: 3362 AN: 4816

European-Finnish (FIN) AF: 0.705 AC: 7439 AN: 10558

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45811 AN: 67954

Other (OTH) AF: 0.647 AC: 1363 AN: 2108

Alfa AF: 0.666 Hom.: 18813

Bravo AF: 0.615

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.41
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3135335; hg19: chr6-32401845;