rs492780

chr2-44916755-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 0.0565 in 152,304 control chromosomes in the GnomAD database, including 300 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 0.056 (300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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 (SAS) allele frequency at 95% confidence interval = 0.105 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: 0.0564 AC: 8578 AN: 152186 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0476

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0565 AC: 8601 AN: 152304 Hom.: 300 Cov.: 32 AF XY: 0.0584 AC XY: 4349 AN XY: 74478

Gnomad4 AFR AF: 0.0348

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0726

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0476

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.0530 Hom.: 251

Bravo AF: 0.0602

Asia WGS AF: 0.0890 AC: 312 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	0.041
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs492780; hg19: chr2-45143894;