rs7690087

Variant names:

• chr4-121581655-T-C
• rs7690087
• XR_939166.2:n.182-17T>C

Variant summary

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

The XR_939166.2(LOC105377401):​n.182-17T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,972 control chromosomes in the GnomAD database, including 30,421 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 0.62 (30421 hom., cov: 31)
• Consequence: LOC105377401 XR_939166.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 5 publications found

Genes affected

LOC105377401 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94323 AN: 151854 Hom.: 30411 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.621 AC: 94375 AN: 151972 Hom.: 30421 Cov.: 31 AF XY: 0.624 AC XY: 46344 AN XY: 74258

African (AFR) AF: 0.432 AC: 17896 AN: 41438

American (AMR) AF: 0.724 AC: 11053 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3468

East Asian (EAS) AF: 0.576 AC: 2971 AN: 5156

South Asian (SAS) AF: 0.590 AC: 2839 AN: 4810

European-Finnish (FIN) AF: 0.745 AC: 7861 AN: 10552

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47574 AN: 67970

Other (OTH) AF: 0.618 AC: 1300 AN: 2102

Alfa AF: 0.665 Hom.: 83082

Bravo AF: 0.613

Asia WGS AF: 0.594 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.54
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs7690087; hg19: chr4-122502810;