chr6-32457105-T-C

Variant names:

• chr6-32457105-T-C
• rs7763262
• ENST00000766007.1:n.162+2715A>G

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.162+2715A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,070 control chromosomes in the GnomAD database, including 38,043 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 0.70 (38043 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 40 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766007.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299747	ENST00000766007.1		n.162+2715A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107110 AN: 151952 Hom.: 38005 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.705 AC: 107203 AN: 152070 Hom.: 38043 Cov.: 31 AF XY: 0.708 AC XY: 52609 AN XY: 74334

African (AFR) AF: 0.721 AC: 29902 AN: 41464

American (AMR) AF: 0.778 AC: 11888 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2982 AN: 3472

East Asian (EAS) AF: 0.738 AC: 3816 AN: 5170

South Asian (SAS) AF: 0.807 AC: 3890 AN: 4820

European-Finnish (FIN) AF: 0.653 AC: 6895 AN: 10556

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45300 AN: 67990

Other (OTH) AF: 0.737 AC: 1555 AN: 2110

Alfa AF: 0.682 Hom.: 128627

Bravo AF: 0.715

Asia WGS AF: 0.739 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.6
DANN	Benign	0.35
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7763262; hg19: chr6-32424882;