rs3135351

Variant names:

• chr6-32425168-C-A
• rs3135351
• ENST00000766247.1:n.283-8924C>A

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.283-8924C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,200 control chromosomes in the GnomAD database, including 1,537 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 0.13 (1537 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 30 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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
ENSG00000299769	ENST00000766247.1	n.283-8924C>A		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.287-200C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19748 AN: 152082 Hom.: 1537 Cov.: 32

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19755 AN: 152200 Hom.: 1537 Cov.: 32 AF XY: 0.128 AC XY: 9525 AN XY: 74388

African (AFR) AF: 0.0651 AC: 2706 AN: 41540

American (AMR) AF: 0.111 AC: 1698 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 314 AN: 3472

East Asian (EAS) AF: 0.113 AC: 584 AN: 5178

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4820

European-Finnish (FIN) AF: 0.204 AC: 2160 AN: 10574

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11538 AN: 68014

Other (OTH) AF: 0.125 AC: 265 AN: 2112

Alfa AF: 0.160 Hom.: 6344

Bravo AF: 0.120

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.72
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs3135351; hg19: chr6-32392945;