chr6-32437082-A-G

Variant names:

• chr6-32437082-A-G
• rs2395173
• ENST00000766007.1:n.279+1062T>C

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.279+1062T>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 152,090 control chromosomes in the GnomAD database, including 30,289 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 (30289 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 47 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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.279+1062T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95041 AN: 151972 Hom.: 30286 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.704

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: 95085 AN: 152090 Hom.: 30289 Cov.: 31 AF XY: 0.630 AC XY: 46846 AN XY: 74340

African (AFR) AF: 0.487 AC: 20198 AN: 41492

American (AMR) AF: 0.659 AC: 10071 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2315 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3698 AN: 5186

South Asian (SAS) AF: 0.698 AC: 3369 AN: 4828

European-Finnish (FIN) AF: 0.704 AC: 7445 AN: 10570

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

European-Non Finnish (NFE) AF: 0.674 AC: 45799 AN: 67958

Other (OTH) AF: 0.647 AC: 1362 AN: 2106

Alfa AF: 0.665 Hom.: 76905

Bravo AF: 0.615

Asia WGS AF: 0.675 AC: 2352 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	5.4
DANN	Benign	0.74
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2395173; hg19: chr6-32404859;