ENST00000775347.1:n.290+12483G>A

Variant names:

• chr7-12082170-C-T
• rs1990602
• ENST00000775347.1:n.290+12483G>A

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.290+12483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 151,998 control chromosomes in the GnomAD database, including 52,210 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 0.83 (52210 hom., cov: 32)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 2 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775347.1. 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
	ENSG00000300984	ENST00000775347.1		n.290+12483G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125482 AN: 151880 Hom.: 52150 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.826 AC: 125597 AN: 151998 Hom.: 52210 Cov.: 32 AF XY: 0.823 AC XY: 61147 AN XY: 74310

African (AFR) AF: 0.868 AC: 36010 AN: 41498

American (AMR) AF: 0.776 AC: 11833 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3468

East Asian (EAS) AF: 0.588 AC: 3038 AN: 5164

South Asian (SAS) AF: 0.674 AC: 3247 AN: 4816

European-Finnish (FIN) AF: 0.841 AC: 8915 AN: 10596

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56891 AN: 67892

Other (OTH) AF: 0.812 AC: 1706 AN: 2102

Alfa AF: 0.831 Hom.: 216999

Bravo AF: 0.826

Asia WGS AF: 0.664 AC: 2307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.52
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs1990602; hg19: chr7-12121796;