rs12360000

Variant names:

• chr10-1855784-G-A
• rs12360000

Your query was ambiguous. Multiple possible variants found:

• chr10-1855784-G-A
• chr10-1855784-G-C
• chr10-1855784-G-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 152,190 control chromosomes in the GnomAD database, including 5,559 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 (5559 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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 (NFE) allele frequency at 95% confidence interval = 0.338 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: 0.243 AC: 36997 AN: 152070 Hom.: 5559 Cov.: 33

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.243 AC: 37003 AN: 152190 Hom.: 5559 Cov.: 33 AF XY: 0.242 AC XY: 17976 AN XY: 74392

Gnomad4 AFR AF: 0.0706

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.234

Alfa AF: 0.168 Hom.: 378

Bravo AF: 0.236

Asia WGS AF: 0.182 AC: 638 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	0.32
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12360000; hg19: chr10-1897978;