3-105317253-A-C

Variant names:

• chr3-105317253-A-C
• rs1920201

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 0.224 in 151,868 control chromosomes in the GnomAD database, including 4,456 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 0.22 (4456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 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: 0.224 AC: 33993 AN: 151750 Hom.: 4453 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.224 AC: 33996 AN: 151868 Hom.: 4456 Cov.: 32 AF XY: 0.230 AC XY: 17080 AN XY: 74204

African (AFR) AF: 0.101 AC: 4199 AN: 41504

American (AMR) AF: 0.200 AC: 3041 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.451 AC: 2328 AN: 5158

South Asian (SAS) AF: 0.319 AC: 1539 AN: 4824

European-Finnish (FIN) AF: 0.331 AC: 3499 AN: 10576

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17493 AN: 67840

Other (OTH) AF: 0.203 AC: 428 AN: 2106

Alfa AF: 0.232 Hom.: 4408

Bravo AF: 0.211

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.64
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1920201; hg19: chr3-105036097;