6-32421528-T-C

Variant names:

• chr6-32421528-T-C
• rs9268557
• ENST00000766247.1:n.282+7158T>C

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+7158T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,114 control chromosomes in the GnomAD database, including 16,800 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 0.46 (16800 hom., cov: 33)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779
• Publications: 40 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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.282+7158T>C		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.287-3840T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70262 AN: 151996 Hom.: 16788 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.462 AC: 70307 AN: 152114 Hom.: 16800 Cov.: 33 AF XY: 0.469 AC XY: 34890 AN XY: 74374

African (AFR) AF: 0.348 AC: 14432 AN: 41484

American (AMR) AF: 0.527 AC: 8066 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3470

East Asian (EAS) AF: 0.561 AC: 2905 AN: 5174

South Asian (SAS) AF: 0.540 AC: 2597 AN: 4810

European-Finnish (FIN) AF: 0.510 AC: 5409 AN: 10596

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33225 AN: 67970

Other (OTH) AF: 0.469 AC: 990 AN: 2112

Alfa AF: 0.478 Hom.: 51101

Bravo AF: 0.457

Asia WGS AF: 0.501 AC: 1741 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	5.2
DANN	Benign	0.34
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs9268557; hg19: chr6-32389305;