rs10853580

Variant names:

• chr18-49527947-A-G
• rs10853580

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 0.177 in 152,112 control chromosomes in the GnomAD database, including 2,514 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 0.18 (2514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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: 0.177 AC: 26885 AN: 151994 Hom.: 2512 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.177 AC: 26900 AN: 152112 Hom.: 2514 Cov.: 32 AF XY: 0.179 AC XY: 13325 AN XY: 74370

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.161

Alfa AF: 0.193 Hom.: 3862

Bravo AF: 0.173

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10853580; hg19: chr18-47054317;