rs1522940

chr3-148597900-C-A

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 0.114 in 152,054 control chromosomes in the GnomAD database, including 1,175 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 0.11 (1175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 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: 0.114 AC: 17262 AN: 151936 Hom.: 1177 Cov.: 32

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.114 AC: 17262 AN: 152054 Hom.: 1175 Cov.: 32 AF XY: 0.117 AC XY: 8681 AN XY: 74324

Gnomad4 AFR AF: 0.0688

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0995

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.113

Alfa AF: 0.117 Hom.: 1153

Bravo AF: 0.120

Asia WGS AF: 0.206 AC: 717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.15
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1522940; hg19: chr3-148315687;