chr2-49827473-A-C

Position:

• chr2-49827473-A-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 0.116 in 151,448 control chromosomes in the GnomAD database, including 1,169 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 0.12 (1169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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: 0.116 AC: 17557 AN: 151330 Hom.: 1168 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.116 AC: 17556 AN: 151448 Hom.: 1169 Cov.: 32 AF XY: 0.113 AC XY: 8366 AN XY: 73992

Gnomad4 AFR AF: 0.0807

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0416 Hom.: 52

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11690625; hg19: chr2-50054611;