chr6-32414163-A-T

Variant names:

• chr6-32414163-A-T
• rs28366194
• ENST00000766247.1:n.151-76A>T

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.151-76A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 152,262 control chromosomes in the GnomAD database, including 770 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 0.088 (770 hom., cov: 30)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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	ENST00000766247.1	n.151-76A>T		intron_variant	Intron 1 of 2
ENSG00000299769	ENST00000766248.1	n.155-76A>T		intron_variant	Intron 1 of 3
ENSG00000299769	ENST00000766249.1	n.150-76A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0878 AC: 13356 AN: 152144 Hom.: 769 Cov.: 30

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0878 AC: 13364 AN: 152262 Hom.: 770 Cov.: 30 AF XY: 0.0845 AC XY: 6289 AN XY: 74460

African (AFR) AF: 0.129 AC: 5358 AN: 41524

American (AMR) AF: 0.105 AC: 1603 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 273 AN: 3472

East Asian (EAS) AF: 0.0626 AC: 325 AN: 5192

South Asian (SAS) AF: 0.0747 AC: 360 AN: 4822

European-Finnish (FIN) AF: 0.0142 AC: 151 AN: 10624

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0735 AC: 4996 AN: 68014

Other (OTH) AF: 0.110 AC: 232 AN: 2114

Alfa AF: 0.0742 Hom.: 60

Bravo AF: 0.0991

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.7
DANN	Benign	0.77
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs28366194; hg19: chr6-32381940;