chr6-32791558-C-A

Variant names:

• chr6-32791558-C-A
• rs2621383
• ENST00000788564.1:n.107-277C>A

Variant summary

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

The ENST00000788564.1(ENSG00000302653):​n.107-277C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,886 control chromosomes in the GnomAD database, including 32,596 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 0.65 (32596 hom., cov: 30)
• Consequence: ENSG00000302653 ENST00000788564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 17 publications found

Genes affected

ENSG00000302653 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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
ENSG00000302653	ENST00000788564.1	n.107-277C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99250 AN: 151768 Hom.: 32577 Cov.: 30

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.654 AC: 99310 AN: 151886 Hom.: 32596 Cov.: 30 AF XY: 0.658 AC XY: 48859 AN XY: 74228

African (AFR) AF: 0.662 AC: 27424 AN: 41406

American (AMR) AF: 0.631 AC: 9632 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2236 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3882 AN: 5156

South Asian (SAS) AF: 0.731 AC: 3515 AN: 4810

European-Finnish (FIN) AF: 0.701 AC: 7392 AN: 10550

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42958 AN: 67920

Other (OTH) AF: 0.651 AC: 1374 AN: 2112

Alfa AF: 0.650 Hom.: 64364

Bravo AF: 0.647

Asia WGS AF: 0.760 AC: 2639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2621383; hg19: chr6-32759335;