chr12-75826838-C-T

Variant names:

• chr12-75826838-C-T
• rs7307780
• ENST00000552856.1:n.296-49308G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000552856.1(ENSG00000258077):​n.296-49308G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,054 control chromosomes in the GnomAD database, including 2,658 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 0.18 (2658 hom., cov: 32)
• Consequence: ENSG00000258077 ENST00000552856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 12 publications found

Genes affected

ENSG00000258077 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000552856.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258077	ENST00000552856.1	TSL:3	n.296-49308G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27658 AN: 151936 Hom.: 2654 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.182 AC: 27689 AN: 152054 Hom.: 2658 Cov.: 32 AF XY: 0.179 AC XY: 13299 AN XY: 74334

African (AFR) AF: 0.219 AC: 9085 AN: 41464

American (AMR) AF: 0.136 AC: 2069 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3472

East Asian (EAS) AF: 0.161 AC: 830 AN: 5166

South Asian (SAS) AF: 0.222 AC: 1065 AN: 4808

European-Finnish (FIN) AF: 0.117 AC: 1239 AN: 10588

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11924 AN: 67982

Other (OTH) AF: 0.177 AC: 373 AN: 2108

Alfa AF: 0.178 Hom.: 9226

Bravo AF: 0.185

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	8.5
DANN	Benign	0.94
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7307780; hg19: chr12-76220618;