rs10502994

Variant names:

• chr18-55135284-C-T
• rs10502994

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 0.262 in 152,034 control chromosomes in the GnomAD database, including 6,060 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 0.26 (6060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 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: 0.262 AC: 39805 AN: 151920 Hom.: 6052 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.262 AC: 39817 AN: 152034 Hom.: 6060 Cov.: 32 AF XY: 0.262 AC XY: 19450 AN XY: 74286

African (AFR) AF: 0.0911 AC: 3777 AN: 41482

American (AMR) AF: 0.325 AC: 4965 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3466

East Asian (EAS) AF: 0.264 AC: 1358 AN: 5146

South Asian (SAS) AF: 0.378 AC: 1825 AN: 4822

European-Finnish (FIN) AF: 0.302 AC: 3196 AN: 10568

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22501 AN: 67960

Other (OTH) AF: 0.299 AC: 631 AN: 2110

Alfa AF: 0.305 Hom.: 18679

Bravo AF: 0.254

Asia WGS AF: 0.336 AC: 1165 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10502994; hg19: chr18-52802515;