rs56148675

Variant names:

• chr2-53529404-T-C
• rs56148675

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0113 AC: 468 AN: 41568

American (AMR) AF: 0.0423 AC: 647 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 71 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0527 AC: 254 AN: 4822

European-Finnish (FIN) AF: 0.0483 AC: 512 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0547 AC: 3723 AN: 68014

Other (OTH) AF: 0.0307 AC: 65 AN: 2114

Alfa AF: 0.0335 Hom.: 36

Bravo AF: 0.0362

Asia WGS AF: 0.0180 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.46
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs56148675; hg19: chr2-53756542;