3-103678925-T-C

Position:

• chr3-103678925-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.103678925T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.313

Alfa AF: 0.245 Hom.: 7335

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12485744; hg19: chr3-103397769;