rs9658628

Variant names:

• chr14-92922041-G-A
• rs9658628

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 0.253 in 151,910 control chromosomes in the GnomAD database, including 5,065 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 (5065 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38508 AN: 151792 Hom.: 5065 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.253 AC: 38505 AN: 151910 Hom.: 5065 Cov.: 30 AF XY: 0.247 AC XY: 18352 AN XY: 74268

African (AFR) AF: 0.256 AC: 10600 AN: 41402

American (AMR) AF: 0.231 AC: 3534 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3468

East Asian (EAS) AF: 0.109 AC: 563 AN: 5164

South Asian (SAS) AF: 0.188 AC: 905 AN: 4806

European-Finnish (FIN) AF: 0.195 AC: 2063 AN: 10554

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18829 AN: 67928

Other (OTH) AF: 0.290 AC: 611 AN: 2106

Alfa AF: 0.269 Hom.: 1989

Bravo AF: 0.257

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.2
DANN	Benign	0.81
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs9658628; hg19: chr14-93388386;