2-57105538-C-T

Variant names:

• chr2-57105538-C-T
• rs1559557

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 0.591 in 151,960 control chromosomes in the GnomAD database, including 26,868 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 0.59 (26868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.591 AC: 89814 AN: 151842 Hom.: 26868 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.591 AC: 89841 AN: 151960 Hom.: 26868 Cov.: 32 AF XY: 0.594 AC XY: 44101 AN XY: 74268

African (AFR) AF: 0.515 AC: 21332 AN: 41442

American (AMR) AF: 0.510 AC: 7771 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3909 AN: 5148

South Asian (SAS) AF: 0.613 AC: 2954 AN: 4822

European-Finnish (FIN) AF: 0.682 AC: 7192 AN: 10550

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42488 AN: 67960

Other (OTH) AF: 0.602 AC: 1272 AN: 2114

Alfa AF: 0.604 Hom.: 46405

Bravo AF: 0.574

Asia WGS AF: 0.673 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1559557; hg19: chr2-57332673;