rs10785350

Variant names:

• chr12-42597336-C-T
• rs10785350

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 0.212 in 152,136 control chromosomes in the GnomAD database, including 3,659 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 0.21 (3659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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: 0.212 AC: 32293 AN: 152018 Hom.: 3651 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.212 AC: 32324 AN: 152136 Hom.: 3659 Cov.: 32 AF XY: 0.209 AC XY: 15545 AN XY: 74384

African (AFR) AF: 0.211 AC: 8758 AN: 41488

American (AMR) AF: 0.167 AC: 2561 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3466

East Asian (EAS) AF: 0.148 AC: 769 AN: 5182

South Asian (SAS) AF: 0.113 AC: 543 AN: 4812

European-Finnish (FIN) AF: 0.212 AC: 2242 AN: 10584

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15821 AN: 67988

Other (OTH) AF: 0.212 AC: 447 AN: 2108

Alfa AF: 0.225 Hom.: 6834

Bravo AF: 0.211

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.012
DANN	Benign	0.66
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10785350; hg19: chr12-42991138;