rs7798002

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr7-25820960-G-A
• chr7-25820960-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000812174.1(ENSG00000286725):​n.297+27966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 152,100 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0020 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812174.1. 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
	ENSG00000286725	ENST00000812174.1		n.297+27966C>T		intron	N/A
	ENSG00000286725	ENST00000812175.1		n.280+27966C>T		intron	N/A
	ENSG00000286725	ENST00000812176.1		n.297+27966C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00196 AC: 298 AN: 151982 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00203

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.000284

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00318

Gnomad OTH AF: 0.00144

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

GnomAD4 genome AF: 0.00196 AC: 298 AN: 152100 Hom.: 0 Cov.: 32 AF XY: 0.00186 AC XY: 138 AN XY: 74332

African (AFR) AF: 0.000482 AC: 20 AN: 41488

American (AMR) AF: 0.00203 AC: 31 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4826

European-Finnish (FIN) AF: 0.000284 AC: 3 AN: 10572

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00318 AC: 216 AN: 67982

Other (OTH) AF: 0.00142 AC: 3 AN: 2110

Alfa AF: 0.000975 Hom.: 167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.40
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7798002;

hg19: chr7-25860580;