7-25820960-G-T

Variant names:

• chr7-25820960-G-T
• rs7798002
• ENST00000812174.1:n.297+27966C>A

Variant summary

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

The ENST00000812174.1(ENSG00000286725):​n.297+27966C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,048 control chromosomes in the GnomAD database, including 3,581 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 0.21 (3581 hom., cov: 32)
• Consequence: ENSG00000286725 ENST00000812174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 7 publications found

Genes affected

ENSG00000286725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 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
ENSG00000286725	ENST00000812174.1	n.297+27966C>A		intron_variant	Intron 2 of 4
ENSG00000286725	ENST00000812175.1	n.280+27966C>A		intron_variant	Intron 2 of 5
ENSG00000286725	ENST00000812176.1	n.297+27966C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31378 AN: 151930 Hom.: 3579 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.207 AC: 31402 AN: 152048 Hom.: 3581 Cov.: 32 AF XY: 0.214 AC XY: 15933 AN XY: 74296

African (AFR) AF: 0.180 AC: 7484 AN: 41478

American (AMR) AF: 0.173 AC: 2637 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2226 AN: 5162

South Asian (SAS) AF: 0.431 AC: 2077 AN: 4816

European-Finnish (FIN) AF: 0.266 AC: 2813 AN: 10568

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13036 AN: 67970

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.101 Hom.: 167

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7798002; hg19: chr7-25860580;