rs12679744

Variant names:

• chr8-74125171-G-A
• rs12679744
• ENST00000668834.2:n.193+31452G>A

Variant summary

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

The ENST00000668834.2(ENSG00000254288):​n.193+31452G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,588 control chromosomes in the GnomAD database, including 17,736 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 0.48 (17736 hom., cov: 29)
• Consequence: ENSG00000254288 ENST00000668834.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 0 publications found

Genes affected

ENSG00000254288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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
ENSG00000254288	ENST00000668834.2	n.193+31452G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72856 AN: 151470 Hom.: 17728 Cov.: 29

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.481 AC: 72905 AN: 151588 Hom.: 17736 Cov.: 29 AF XY: 0.478 AC XY: 35380 AN XY: 74028

African (AFR) AF: 0.482 AC: 19912 AN: 41306

American (AMR) AF: 0.449 AC: 6836 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3152 AN: 5134

South Asian (SAS) AF: 0.501 AC: 2392 AN: 4778

European-Finnish (FIN) AF: 0.408 AC: 4277 AN: 10474

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32847 AN: 67886

Other (OTH) AF: 0.494 AC: 1039 AN: 2102

Alfa AF: 0.477 Hom.: 16655

Bravo AF: 0.486

Asia WGS AF: 0.555 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.63
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs12679744; hg19: chr8-75037406;