chr10-3820748-T-C

Variant names:

• chr10-3820748-T-C
• rs12266938

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 0.248 in 152,150 control chromosomes in the GnomAD database, including 5,628 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 0.25 (5628 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.248 AC: 37758 AN: 152030 Hom.: 5617 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.248 AC: 37801 AN: 152150 Hom.: 5628 Cov.: 33 AF XY: 0.254 AC XY: 18928 AN XY: 74388

African (AFR) AF: 0.392 AC: 16255 AN: 41480

American (AMR) AF: 0.294 AC: 4492 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1975 AN: 5178

South Asian (SAS) AF: 0.339 AC: 1632 AN: 4816

European-Finnish (FIN) AF: 0.189 AC: 2004 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9843 AN: 68006

Other (OTH) AF: 0.245 AC: 518 AN: 2110

Alfa AF: 0.185 Hom.: 6987

Bravo AF: 0.265

Asia WGS AF: 0.371 AC: 1290 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.52
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs12266938; hg19: chr10-3862940;