rs7786598

Variant names:

• chr7-130344137-G-A
• rs7786598
• XR_927965.4:n.591C>T

Variant summary

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

The XR_927965.4(LOC105375503):​n.591C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,054 control chromosomes in the GnomAD database, including 25,227 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 0.57 (25227 hom., cov: 33)
• Consequence: LOC105375503 XR_927965.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 4 publications found

Genes affected

LOC105375503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87241 AN: 151936 Hom.: 25218 Cov.: 33

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.574 AC: 87288 AN: 152054 Hom.: 25227 Cov.: 33 AF XY: 0.572 AC XY: 42482 AN XY: 74328

African (AFR) AF: 0.612 AC: 25357 AN: 41456

American (AMR) AF: 0.601 AC: 9198 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2060 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2773 AN: 5168

South Asian (SAS) AF: 0.556 AC: 2675 AN: 4814

European-Finnish (FIN) AF: 0.539 AC: 5692 AN: 10562

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.554 AC: 37683 AN: 67982

Other (OTH) AF: 0.586 AC: 1237 AN: 2112

Alfa AF: 0.570 Hom.: 4419

Bravo AF: 0.579

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7786598; hg19: chr7-129983977;