rs7686928

Variant names:

• chr4-187812675-C-T
• rs7686928

Variant summary

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

The variant allele was found at a frequency of 0.247 in 152,058 control chromosomes in the GnomAD database, including 7,064 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 0.25 (7064 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37533 AN: 151940 Hom.: 7045 Cov.: 33

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.247 AC: 37599 AN: 152058 Hom.: 7064 Cov.: 33 AF XY: 0.241 AC XY: 17905 AN XY: 74330

African (AFR) AF: 0.526 AC: 21804 AN: 41436

American (AMR) AF: 0.160 AC: 2441 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 780 AN: 3468

East Asian (EAS) AF: 0.132 AC: 679 AN: 5160

South Asian (SAS) AF: 0.207 AC: 999 AN: 4822

European-Finnish (FIN) AF: 0.0717 AC: 760 AN: 10602

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9476 AN: 67982

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.180 Hom.: 1300

Bravo AF: 0.264

Asia WGS AF: 0.203 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.18
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs7686928; hg19: chr4-188733829;