12-27855836-T-G

Variant names:

• chr12-27855836-T-G
• rs258401
• ENST00000825469.1:n.320+44746T>G

Variant summary

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

The ENST00000825469.1(ENSG00000257042):​n.320+44746T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,032 control chromosomes in the GnomAD database, including 48,314 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 0.79 (48314 hom., cov: 30)
• Consequence: ENSG00000257042 ENST00000825469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 7 publications found

Genes affected

ENSG00000257042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 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
ENSG00000257042	ENST00000825469.1	n.320+44746T>G		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825470.1	n.175+44746T>G		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825471.1	n.140+44746T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120045 AN: 151914 Hom.: 48272 Cov.: 30

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.790 AC: 120136 AN: 152032 Hom.: 48314 Cov.: 30 AF XY: 0.781 AC XY: 58012 AN XY: 74260

African (AFR) AF: 0.948 AC: 39332 AN: 41506

American (AMR) AF: 0.681 AC: 10391 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2865 AN: 3472

East Asian (EAS) AF: 0.770 AC: 3968 AN: 5150

South Asian (SAS) AF: 0.686 AC: 3305 AN: 4820

European-Finnish (FIN) AF: 0.659 AC: 6942 AN: 10530

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50752 AN: 67966

Other (OTH) AF: 0.793 AC: 1679 AN: 2116

Alfa AF: 0.773 Hom.: 49511

Bravo AF: 0.800

Asia WGS AF: 0.733 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs258401; hg19: chr12-28008769;