rs10989692

Variant names:

• chr9-101912273-G-A
• rs10989692

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 0.145 in 152,044 control chromosomes in the GnomAD database, including 2,414 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 0.15 (2414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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: 0.145 AC: 22039 AN: 151926 Hom.: 2408 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.0159

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0549

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.145 AC: 22056 AN: 152044 Hom.: 2414 Cov.: 32 AF XY: 0.139 AC XY: 10304 AN XY: 74340

African (AFR) AF: 0.302 AC: 12529 AN: 41462

American (AMR) AF: 0.0866 AC: 1323 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 308 AN: 3472

East Asian (EAS) AF: 0.0159 AC: 82 AN: 5160

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4826

European-Finnish (FIN) AF: 0.0549 AC: 582 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6690 AN: 67946

Other (OTH) AF: 0.134 AC: 282 AN: 2104

Alfa AF: 0.116 Hom.: 486

Bravo AF: 0.154

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10989692; hg19: chr9-104674555;