3-103526248-C-T

Variant names:

• chr3-103526248-C-T
• rs1397924

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 0.419 in 151,880 control chromosomes in the GnomAD database, including 15,288 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 0.42 (15288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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: 0.419 AC: 63519 AN: 151762 Hom.: 15240 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.419 AC: 63635 AN: 151880 Hom.: 15288 Cov.: 32 AF XY: 0.423 AC XY: 31365 AN XY: 74224

African (AFR) AF: 0.666 AC: 27578 AN: 41412

American (AMR) AF: 0.427 AC: 6516 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1311 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1473 AN: 5144

South Asian (SAS) AF: 0.476 AC: 2293 AN: 4820

European-Finnish (FIN) AF: 0.310 AC: 3260 AN: 10530

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20038 AN: 67942

Other (OTH) AF: 0.419 AC: 883 AN: 2108

Alfa AF: 0.335 Hom.: 35276

Bravo AF: 0.437

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.46
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs1397924; hg19: chr3-103245092;