12-128062664-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287311 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000287311	ENST00000666596.1	n.85+5613G>A		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.440

Alfa AF: 0.343 Hom.: 1387

Bravo AF: 0.401

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7300686; hg19: chr12-128547209;