rs10988496

Variant names:

• chr9-129755222-A-G
• rs10988496

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 0.221 in 151,998 control chromosomes in the GnomAD database, including 5,563 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 0.22 (5563 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 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: 0.220 AC: 33438 AN: 151880 Hom.: 5530 Cov.: 31

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.221 AC: 33517 AN: 151998 Hom.: 5563 Cov.: 31 AF XY: 0.216 AC XY: 16056 AN XY: 74320

African (AFR) AF: 0.469 AC: 19437 AN: 41440

American (AMR) AF: 0.132 AC: 2012 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3468

East Asian (EAS) AF: 0.144 AC: 740 AN: 5150

South Asian (SAS) AF: 0.205 AC: 990 AN: 4818

European-Finnish (FIN) AF: 0.0700 AC: 741 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8636 AN: 67972

Other (OTH) AF: 0.206 AC: 432 AN: 2100

Alfa AF: 0.146 Hom.: 1721

Bravo AF: 0.235

Asia WGS AF: 0.238 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.88
DANN	Benign	0.43
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10988496; hg19: chr9-132517501; COSMIC: COSV107427558;