rs7756262

Variant names:

• chr6-32430898-T-A
• rs7756262
• ENST00000766248.1:n.576T>A

Variant summary

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

The ENST00000766248.1(ENSG00000299769):​n.576T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,960 control chromosomes in the GnomAD database, including 11,678 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 0.39 (11678 hom., cov: 31)
• Consequence: ENSG00000299769 ENST00000766248.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.879
• Publications: 16 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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	ENST00000766248.1	n.576T>A		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000299747	ENST00000766007.1	n.280-167A>T		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-3194T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58695 AN: 151842 Hom.: 11677 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.386 AC: 58716 AN: 151960 Hom.: 11678 Cov.: 31 AF XY: 0.389 AC XY: 28867 AN XY: 74276

African (AFR) AF: 0.341 AC: 14133 AN: 41408

American (AMR) AF: 0.447 AC: 6819 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2854 AN: 5170

South Asian (SAS) AF: 0.521 AC: 2511 AN: 4820

European-Finnish (FIN) AF: 0.290 AC: 3060 AN: 10566

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26175 AN: 67954

Other (OTH) AF: 0.411 AC: 867 AN: 2108

Alfa AF: 0.380 Hom.: 1364

Bravo AF: 0.395

Asia WGS AF: 0.472 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.70
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs7756262; hg19: chr6-32398675;