rs8012339

Variant names:

• chr14-60330827-T-G
• rs8012339
• ENST00000741815.1:n.267-12590A>C

Variant summary

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

The ENST00000741815.1(ENSG00000296765):​n.267-12590A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,210 control chromosomes in the GnomAD database, including 1,300 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 0.11 (1300 hom., cov: 32)
• Consequence: ENSG00000296765 ENST00000741815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 5 publications found

Genes affected

ENSG00000296765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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
ENSG00000296765	ENST00000741815.1	n.267-12590A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17500 AN: 152092 Hom.: 1304 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0901

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.115 AC: 17504 AN: 152210 Hom.: 1300 Cov.: 32 AF XY: 0.114 AC XY: 8471 AN XY: 74432

African (AFR) AF: 0.187 AC: 7760 AN: 41514

American (AMR) AF: 0.0898 AC: 1373 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3470

East Asian (EAS) AF: 0.122 AC: 630 AN: 5170

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4818

European-Finnish (FIN) AF: 0.0274 AC: 291 AN: 10618

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0804 AC: 5470 AN: 68012

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.0990 Hom.: 513

Bravo AF: 0.120

Asia WGS AF: 0.174 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs8012339; hg19: chr14-60797545;