rs7307780

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369844	XR_007063374.1	n.236+7695G>A		intron_variant	Intron 1 of 6
LOC105369844	XR_007063375.1	n.236+7695G>A		intron_variant	Intron 1 of 15
LOC105369844	XR_007063376.1	n.236+7695G>A		intron_variant	Intron 1 of 7
LOC105369844	XR_007063377.1	n.236+7695G>A		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258077	ENST00000552856.1	n.296-49308G>A		intron_variant	Intron 1 of 4	3

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 v4.3

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;