ENST00000766007.1:n.163-7508C>T

Variant names:

• chr6-32445768-G-A
• rs3129889
• ENST00000766007.1:n.163-7508C>T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.163-7508C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,218 control chromosomes in the GnomAD database, including 62,668 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 0.91 (62668 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 95 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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.163-7508C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137815 AN: 152100 Hom.: 62615 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.906 AC: 137926 AN: 152218 Hom.: 62668 Cov.: 31 AF XY: 0.908 AC XY: 67543 AN XY: 74416

African (AFR) AF: 0.953 AC: 39604 AN: 41542

American (AMR) AF: 0.928 AC: 14194 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3395 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5161 AN: 5180

South Asian (SAS) AF: 0.981 AC: 4732 AN: 4826

European-Finnish (FIN) AF: 0.871 AC: 9229 AN: 10594

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58528 AN: 67992

Other (OTH) AF: 0.933 AC: 1973 AN: 2114

Alfa AF: 0.883 Hom.: 232943

Bravo AF: 0.913

Asia WGS AF: 0.982 AC: 3414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.27
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3129889; hg19: chr6-32413545;