rs10871777

Positions:

• chr18-60184530-A-G
• chr18-60184530-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 0.243 in 152,134 control chromosomes in the GnomAD database, including 4,687 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 0.24 (4687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36867 AN: 152024 Hom.: 4685 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.243 AC: 36905 AN: 152134 Hom.: 4687 Cov.: 32 AF XY: 0.239 AC XY: 17748 AN XY: 74374

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.229

Alfa AF: 0.241 Hom.: 6881

Bravo AF: 0.242

Asia WGS AF: 0.227 AC: 792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10871777; hg19: chr18-57851763;