12-128062664-C-T

Variant names:

• chr12-128062664-C-T
• rs7300686
• ENST00000666596.1:n.85+5613G>A

Variant summary

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

The ENST00000666596.1(ENSG00000287311):​n.85+5613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,014 control chromosomes in the GnomAD database, including 14,730 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 0.41 (14730 hom., cov: 33)
• Consequence: ENSG00000287311 ENST00000666596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 3 publications found

Genes affected

ENSG00000287311 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666596.1. 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
	ENSG00000287311	ENST00000666596.1		n.85+5613G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62558 AN: 151896 Hom.: 14729 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.412 AC: 62569 AN: 152014 Hom.: 14730 Cov.: 33 AF XY: 0.413 AC XY: 30682 AN XY: 74294

African (AFR) AF: 0.181 AC: 7493 AN: 41460

American (AMR) AF: 0.535 AC: 8174 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1643 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1356 AN: 5172

South Asian (SAS) AF: 0.451 AC: 2175 AN: 4820

European-Finnish (FIN) AF: 0.503 AC: 5298 AN: 10532

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 35015 AN: 67968

Other (OTH) AF: 0.440 AC: 929 AN: 2112

Alfa AF: 0.430 Hom.: 4072

Bravo AF: 0.401

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.47
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7300686; hg19: chr12-128547209;