rs1492078

Positions:

• chr3-148697390-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 0.515 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;