12-126640834-C-T

Variant names:

• chr12-126640834-C-T
• rs2347306
• ENST00000541769.1:n.368+6536G>A

Variant summary

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

The ENST00000545853.1(ENSG00000256732):​n.227-30571G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,284 control chromosomes in the GnomAD database, including 64,736 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 0.92 (64736 hom., cov: 33)
• Consequence: ENSG00000256732 ENST00000545853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

ENSG00000255944 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.953 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
ENSG00000255944	ENST00000541769.1	n.368+6536G>A		intron_variant	Intron 2 of 2	5
ENSG00000256732	ENST00000545853.1	n.227-30571G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140219 AN: 152166 Hom.: 64719 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.921 AC: 140282 AN: 152284 Hom.: 64736 Cov.: 33 AF XY: 0.922 AC XY: 68636 AN XY: 74464

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.926

Alfa AF: 0.934 Hom.: 10712

Bravo AF: 0.917

Asia WGS AF: 0.913 AC: 3174 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	1.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2347306; hg19: chr12-127125380;