chr3-103526248-C-T

Variant names:

• chr3-103526248-C-T
• rs1397924

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 0.419 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.419

Alfa AF: 0.317 Hom.: 13529

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1397924; hg19: chr3-103245092;