chr6-32452402-C-T

Variant names:

• chr6-32452402-C-T
• rs7754768
• ENST00000766007.1:n.162+7418G>A

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.162+7418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,818 control chromosomes in the GnomAD database, including 24,808 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 0.57 (24808 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 35 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 (AMR) allele frequency at 95% confidence interval = 0.635 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.162+7418G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 85956 AN: 151700 Hom.: 24796 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.567 AC: 86008 AN: 151818 Hom.: 24808 Cov.: 32 AF XY: 0.566 AC XY: 42025 AN XY: 74196

African (AFR) AF: 0.486 AC: 20125 AN: 41382

American (AMR) AF: 0.646 AC: 9848 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2960 AN: 5166

South Asian (SAS) AF: 0.637 AC: 3072 AN: 4826

European-Finnish (FIN) AF: 0.504 AC: 5297 AN: 10520

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.589 AC: 39990 AN: 67900

Other (OTH) AF: 0.604 AC: 1273 AN: 2106

Alfa AF: 0.583 Hom.: 80818

Bravo AF: 0.576

Asia WGS AF: 0.542 AC: 1888 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	2.6
DANN	Benign	0.39
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7754768; hg19: chr6-32420179; COSMIC: COSV51803812;