rs56148675

chr2-53529404-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 0.0387 in 152,282 control chromosomes in the GnomAD database, including 138 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 0.039 (138 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174

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 (NFE) allele frequency at 95% confidence interval = 0.0533 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: 0.0387 AC: 5890 AN: 152164 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0387 AC: 5896 AN: 152282 Hom.: 138 Cov.: 31 AF XY: 0.0386 AC XY: 2876 AN XY: 74462

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0527

Gnomad4 FIN AF: 0.0483

Gnomad4 NFE AF: 0.0547

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0442 Hom.: 13

Bravo AF: 0.0362

Asia WGS AF: 0.0180 AC: 61 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	2.7
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56148675; hg19: chr2-53756542;