3-148697390-T-C

Variant names:

• chr3-148697390-T-C
• rs1492078

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 0.515 in 152,048 control chromosomes in the GnomAD database, including 23,991 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 0.51 (23991 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

ACMG classification

Verdict is Benign. Variant got -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 = 0.792 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: 0.515 AC: 78233 AN: 151930 Hom.: 23980 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.515 AC: 78249 AN: 152048 Hom.: 23991 Cov.: 31 AF XY: 0.521 AC XY: 38759 AN XY: 74328

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.524

Alfa AF: 0.536 Hom.: 2323

Bravo AF: 0.503

Asia WGS AF: 0.660 AC: 2293 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	2.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1492078; hg19: chr3-148415177;