chr2-53529404-T-C

Variant names:

• chr2-53529404-T-C
• rs56148675

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;