chr10-1855784-G-A

Variant names:

• chr10-1855784-G-A
• rs12360000

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0706 AC: 2934 AN: 41558

American (AMR) AF: 0.288 AC: 4406 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3470

East Asian (EAS) AF: 0.173 AC: 892 AN: 5170

South Asian (SAS) AF: 0.201 AC: 970 AN: 4820

European-Finnish (FIN) AF: 0.310 AC: 3279 AN: 10590

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23226 AN: 67970

Other (OTH) AF: 0.234 AC: 493 AN: 2108

Alfa AF: 0.232 Hom.: 1353

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12360000; hg19: chr10-1897978;