3-103678925-T-C

Variant names:

• chr3-103678925-T-C
• rs12485744

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 0.324 in 151,086 control chromosomes in the GnomAD database, including 8,591 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 0.32 (8591 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 6 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 = 0.434 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: 0.324 AC: 48909 AN: 150968 Hom.: 8551 Cov.: 30

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.324 AC: 49001 AN: 151086 Hom.: 8591 Cov.: 30 AF XY: 0.334 AC XY: 24641 AN XY: 73752

African (AFR) AF: 0.439 AC: 18125 AN: 41242

American (AMR) AF: 0.374 AC: 5646 AN: 15102

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 948 AN: 3458

East Asian (EAS) AF: 0.305 AC: 1555 AN: 5100

South Asian (SAS) AF: 0.410 AC: 1971 AN: 4804

European-Finnish (FIN) AF: 0.371 AC: 3893 AN: 10502

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 15997 AN: 67580

Other (OTH) AF: 0.313 AC: 657 AN: 2096

Alfa AF: 0.263 Hom.: 20078

Bravo AF: 0.329

Asia WGS AF: 0.421 AC: 1460 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs12485744; hg19: chr3-103397769;