12-69723466-C-T

Variant names:

• chr12-69723466-C-T
• rs775450
• ENST00000501387.7:n.592+1756G>A

Variant summary

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

The ENST00000501387.7(ENSG00000247131):​n.592+1756G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,872 control chromosomes in the GnomAD database, including 9,459 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 0.35 (9459 hom., cov: 31)
• Consequence: ENSG00000247131 ENST00000501387.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 11 publications found

Genes affected

ENSG00000247131 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928002	NR_110072.2	n.565+1756G>A		intron_variant	Intron 3 of 3
LOC101928002	NR_159971.1	n.442-895G>A		intron_variant	Intron 2 of 2
LOC101928002	NR_159972.1	n.441+1756G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000247131	ENST00000501387.7	n.592+1756G>A		intron_variant	Intron 3 of 3	1
ENSG00000247131	ENST00000501300.2	n.489-895G>A		intron_variant	Intron 2 of 2	5
ENSG00000247131	ENST00000661191.2	n.514+1756G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52906 AN: 151754 Hom.: 9452 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.349 AC: 52937 AN: 151872 Hom.: 9459 Cov.: 31 AF XY: 0.351 AC XY: 26030 AN XY: 74198

African (AFR) AF: 0.325 AC: 13460 AN: 41420

American (AMR) AF: 0.312 AC: 4751 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1289 AN: 5162

South Asian (SAS) AF: 0.366 AC: 1758 AN: 4806

European-Finnish (FIN) AF: 0.407 AC: 4278 AN: 10508

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25297 AN: 67942

Other (OTH) AF: 0.325 AC: 687 AN: 2116

Alfa AF: 0.356 Hom.: 16528

Bravo AF: 0.334

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.047
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs775450; hg19: chr12-70117246;