rs9556658

Variant names:

• chr13-97025997-A-G
• rs9556658

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 0.258 in 152,090 control chromosomes in the GnomAD database, including 7,667 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 0.26 (7667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.258 AC: 39211 AN: 151972 Hom.: 7640 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.258 AC: 39294 AN: 152090 Hom.: 7667 Cov.: 32 AF XY: 0.255 AC XY: 18968 AN XY: 74374

African (AFR) AF: 0.552 AC: 22881 AN: 41428

American (AMR) AF: 0.147 AC: 2245 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1129 AN: 5178

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4820

European-Finnish (FIN) AF: 0.121 AC: 1287 AN: 10600

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9198 AN: 67996

Other (OTH) AF: 0.237 AC: 499 AN: 2108

Alfa AF: 0.186 Hom.: 2029

Bravo AF: 0.270

Asia WGS AF: 0.284 AC: 989 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	1.6
DANN	Benign	0.45
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs9556658; hg19: chr13-97678251;