rs12679744

Positions:

• chr8-74125171-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668834.1(ENSG00000253983):​n.175+31452G>A variant causes a intron, non coding transcript 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: ENST00000668834.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668834.1	n.175+31452G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.494

Alfa AF: 0.478 Hom.: 10059

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12679744; hg19: chr8-75037406;