rs12665321

Variant names:

• chr6-86059571-C-A
• rs12665321
• ENST00000755499.1:n.386-8022C>A

Variant summary

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

The ENST00000755499.1(ENSG00000288021):​n.386-8022C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,528 control chromosomes in the GnomAD database, including 5,117 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 0.23 (5117 hom., cov: 31)
• Consequence: ENSG00000288021 ENST00000755499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.986
• Publications: 3 publications found

Genes affected

ENSG00000288021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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
ENSG00000288021	ENST00000755499.1	n.386-8022C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35580 AN: 151412 Hom.: 5117 Cov.: 31

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.235 AC: 35578 AN: 151528 Hom.: 5117 Cov.: 31 AF XY: 0.233 AC XY: 17270 AN XY: 73992

African (AFR) AF: 0.0843 AC: 3483 AN: 41340

American (AMR) AF: 0.171 AC: 2601 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3464

East Asian (EAS) AF: 0.336 AC: 1730 AN: 5144

South Asian (SAS) AF: 0.156 AC: 748 AN: 4804

European-Finnish (FIN) AF: 0.358 AC: 3734 AN: 10426

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21768 AN: 67836

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.277 Hom.: 806

Bravo AF: 0.214

Asia WGS AF: 0.227 AC: 788 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs12665321; hg19: chr6-86769289;