rs498693

Variant names:

• chr9-110857689-T-A
• rs498693

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 0.229 in 152,024 control chromosomes in the GnomAD database, including 4,519 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 0.23 (4519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.229 AC: 34798 AN: 151906 Hom.: 4506 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.229 AC: 34862 AN: 152024 Hom.: 4519 Cov.: 32 AF XY: 0.230 AC XY: 17066 AN XY: 74328

African (AFR) AF: 0.323 AC: 13383 AN: 41436

American (AMR) AF: 0.273 AC: 4176 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 855 AN: 3464

East Asian (EAS) AF: 0.312 AC: 1608 AN: 5162

South Asian (SAS) AF: 0.225 AC: 1087 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1412 AN: 10590

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11657 AN: 67952

Other (OTH) AF: 0.256 AC: 540 AN: 2110

Alfa AF: 0.209 Hom.: 454

Bravo AF: 0.247

Asia WGS AF: 0.285 AC: 989 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	4.1
DANN	Benign	0.56
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs498693; hg19: chr9-113619969; COSMIC: COSV60394147;