6-32432311-C-T

Variant names:

• chr6-32432311-C-T
• rs984778
• ENST00000766007.1:n.280-1580G>A

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-1580G>A 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 151,726 control chromosomes in the GnomAD database, including 30,195 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 (30195 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 38 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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.280-1580G>A		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-1781C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94829 AN: 151608 Hom.: 30192 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.625 AC: 94873 AN: 151726 Hom.: 30195 Cov.: 31 AF XY: 0.630 AC XY: 46724 AN XY: 74136

African (AFR) AF: 0.486 AC: 20109 AN: 41336

American (AMR) AF: 0.659 AC: 10044 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2308 AN: 3462

East Asian (EAS) AF: 0.714 AC: 3666 AN: 5136

South Asian (SAS) AF: 0.697 AC: 3367 AN: 4828

European-Finnish (FIN) AF: 0.705 AC: 7434 AN: 10538

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.674 AC: 45756 AN: 67880

Other (OTH) AF: 0.648 AC: 1363 AN: 2102

Alfa AF: 0.658 Hom.: 55504

Bravo AF: 0.615

Asia WGS AF: 0.673 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.38
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs984778; hg19: chr6-32400088;