rs10502774

Variant names:

• chr18-41674056-A-C
• rs10502774

Your query was ambiguous. Multiple possible variants found:

• chr18-41674056-A-C
• chr18-41674056-A-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 0.146 in 152,140 control chromosomes in the GnomAD database, including 2,051 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 0.15 (2051 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 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: 0.146 AC: 22255 AN: 152022 Hom.: 2051 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0948

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.146 AC: 22263 AN: 152140 Hom.: 2051 Cov.: 32 AF XY: 0.149 AC XY: 11105 AN XY: 74370

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0948

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0642 Hom.: 83

Bravo AF: 0.153

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502774; hg19: chr18-39254020;