2-657954-C-T

Variant names:

• chr2-657954-C-T
• rs17042288

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 0.335 in 151,938 control chromosomes in the GnomAD database, including 8,998 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 0.34 (8998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 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: 0.335 AC: 50908 AN: 151820 Hom.: 8987 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.335 AC: 50951 AN: 151938 Hom.: 8998 Cov.: 32 AF XY: 0.340 AC XY: 25276 AN XY: 74248

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.316

Alfa AF: 0.313 Hom.: 3880

Bravo AF: 0.343

Asia WGS AF: 0.500 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17042288; hg19: chr2-657954;