rs763035

Variant names:

• chr6-32427068-G-A
• rs763035
• ENST00000766247.1:n.283-7024G>A

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.283-7024G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,092 control chromosomes in the GnomAD database, including 1,535 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 (1535 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 14 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=-0.99).
• 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.283-7024G>A		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.391+1596G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19669 AN: 151974 Hom.: 1535 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0791

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.129 AC: 19676 AN: 152092 Hom.: 1535 Cov.: 32 AF XY: 0.128 AC XY: 9488 AN XY: 74352

African (AFR) AF: 0.0651 AC: 2699 AN: 41484

American (AMR) AF: 0.109 AC: 1669 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0773 AC: 268 AN: 3468

East Asian (EAS) AF: 0.113 AC: 583 AN: 5180

South Asian (SAS) AF: 0.0785 AC: 379 AN: 4826

European-Finnish (FIN) AF: 0.205 AC: 2166 AN: 10546

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

European-Non Finnish (NFE) AF: 0.170 AC: 11538 AN: 67984

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.145 Hom.: 247

Bravo AF: 0.120

Asia WGS AF: 0.114 AC: 394 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.82
DANN	Benign	0.45
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs763035; hg19: chr6-32394845;