rs10502994

chr18-55135284-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0911

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.299

Alfa AF: 0.321 Hom.: 12068

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502994; hg19: chr18-52802515;