rs12676327

Variant names:

• chr8-29639246-T-G
• rs12676327
• ENST00000771089.1:n.142+1258T>G

Variant summary

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

The ENST00000771089.1(ENSG00000300341):​n.142+1258T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,984 control chromosomes in the GnomAD database, including 25,592 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 0.56 (25592 hom., cov: 31)
• Consequence: ENSG00000300341 ENST00000771089.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 3 publications found

Genes affected

ENSG00000300341 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.728 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
ENSG00000300341	ENST00000771089.1	n.142+1258T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84511 AN: 151864 Hom.: 25595 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.556 AC: 84537 AN: 151984 Hom.: 25592 Cov.: 31 AF XY: 0.562 AC XY: 41760 AN XY: 74312

African (AFR) AF: 0.302 AC: 12497 AN: 41434

American (AMR) AF: 0.653 AC: 9968 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3593 AN: 5166

South Asian (SAS) AF: 0.748 AC: 3601 AN: 4814

European-Finnish (FIN) AF: 0.630 AC: 6656 AN: 10572

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44130 AN: 67946

Other (OTH) AF: 0.573 AC: 1207 AN: 2106

Alfa AF: 0.620 Hom.: 24482

Bravo AF: 0.539

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.76
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs12676327; hg19: chr8-29496762;