rs9658629

Variant names:

• chr14-92922129-A-T
• rs9658629

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 0.129 in 152,172 control chromosomes in the GnomAD database, including 1,310 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 0.13 (1310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 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: 0.129 AC: 19681 AN: 152054 Hom.: 1302 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.129 AC: 19705 AN: 152172 Hom.: 1310 Cov.: 31 AF XY: 0.133 AC XY: 9909 AN XY: 74394

African (AFR) AF: 0.131 AC: 5424 AN: 41504

American (AMR) AF: 0.0861 AC: 1317 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3472

East Asian (EAS) AF: 0.132 AC: 683 AN: 5176

South Asian (SAS) AF: 0.215 AC: 1035 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1934 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8473 AN: 67990

Other (OTH) AF: 0.120 AC: 253 AN: 2114

Alfa AF: 0.127 Hom.: 173

Bravo AF: 0.119

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.091
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9658629; hg19: chr14-93388474;