rs10988449

Variant names:

• chr9-129608081-C-T
• rs10988449

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 0.184 in 151,946 control chromosomes in the GnomAD database, including 3,264 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 0.18 (3264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 16 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 = 0.331 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: 0.184 AC: 27944 AN: 151842 Hom.: 3259 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.184 AC: 27985 AN: 151946 Hom.: 3264 Cov.: 32 AF XY: 0.179 AC XY: 13293 AN XY: 74274

African (AFR) AF: 0.336 AC: 13887 AN: 41360

American (AMR) AF: 0.133 AC: 2036 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3468

East Asian (EAS) AF: 0.0519 AC: 268 AN: 5164

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4826

European-Finnish (FIN) AF: 0.0891 AC: 941 AN: 10560

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9182 AN: 67974

Other (OTH) AF: 0.174 AC: 365 AN: 2102

Alfa AF: 0.152 Hom.: 8058

Bravo AF: 0.197

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.47
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10988449; hg19: chr9-132370360;