rs10880785

Variant names:

• chr12-38261603-T-G
• rs10880785

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 0.301 in 152,014 control chromosomes in the GnomAD database, including 8,873 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 0.30 (8873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 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: 0.301 AC: 45713 AN: 151896 Hom.: 8871 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.301 AC: 45707 AN: 152014 Hom.: 8873 Cov.: 32 AF XY: 0.299 AC XY: 22230 AN XY: 74284

African (AFR) AF: 0.0880 AC: 3652 AN: 41502

American (AMR) AF: 0.279 AC: 4255 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3468

East Asian (EAS) AF: 0.0312 AC: 161 AN: 5166

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4812

European-Finnish (FIN) AF: 0.477 AC: 5036 AN: 10554

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29272 AN: 67928

Other (OTH) AF: 0.284 AC: 599 AN: 2108

Alfa AF: 0.393 Hom.: 8350

Bravo AF: 0.279

Asia WGS AF: 0.146 AC: 510 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10880785; hg19: chr12-38655405;