12-115114632-A-G

Variant names:

• chr12-115114632-A-G
• rs35444
• ENST00000812050.1:n.250+10246A>G

Variant summary

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

The ENST00000812050.1(ENSG00000305627):​n.250+10246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,046 control chromosomes in the GnomAD database, including 11,189 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 0.38 (11189 hom., cov: 32)
• Consequence: ENSG00000305627 ENST00000812050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 40 publications found

Genes affected

ENSG00000305627 (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 = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812050.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305627	ENST00000812050.1		n.250+10246A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58047 AN: 151928 Hom.: 11177 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.382 AC: 58088 AN: 152046 Hom.: 11189 Cov.: 32 AF XY: 0.381 AC XY: 28292 AN XY: 74326

African (AFR) AF: 0.408 AC: 16924 AN: 41456

American (AMR) AF: 0.360 AC: 5504 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1064 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5172

South Asian (SAS) AF: 0.464 AC: 2235 AN: 4816

European-Finnish (FIN) AF: 0.358 AC: 3774 AN: 10556

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26027 AN: 67978

Other (OTH) AF: 0.394 AC: 834 AN: 2116

Alfa AF: 0.383 Hom.: 48453

Bravo AF: 0.380

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.29
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs35444; hg19: chr12-115552437;