rs10502692

Variant names:

• chr18-38460388-C-T
• rs10502692

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 0.214 in 151,906 control chromosomes in the GnomAD database, including 3,657 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 0.21 (3657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.222 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: 0.214 AC: 32534 AN: 151792 Hom.: 3648 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.214 AC: 32570 AN: 151906 Hom.: 3657 Cov.: 32 AF XY: 0.216 AC XY: 16044 AN XY: 74212

African (AFR) AF: 0.226 AC: 9346 AN: 41422

American (AMR) AF: 0.225 AC: 3440 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3464

East Asian (EAS) AF: 0.227 AC: 1172 AN: 5156

South Asian (SAS) AF: 0.204 AC: 983 AN: 4818

European-Finnish (FIN) AF: 0.206 AC: 2162 AN: 10494

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14189 AN: 67970

Other (OTH) AF: 0.214 AC: 452 AN: 2108

Alfa AF: 0.211 Hom.: 8566

Bravo AF: 0.219

Asia WGS AF: 0.242 AC: 838 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs10502692; hg19: chr18-36040352;