2-657954-C-T

Variant names:

• chr2-657954-C-T
• rs17042288

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 0.335 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 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: 0.335 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

African (AFR) AF: 0.344 AC: 14247 AN: 41414

American (AMR) AF: 0.407 AC: 6213 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2770 AN: 5148

South Asian (SAS) AF: 0.541 AC: 2601 AN: 4804

European-Finnish (FIN) AF: 0.299 AC: 3162 AN: 10564

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20209 AN: 67964

Other (OTH) AF: 0.316 AC: 665 AN: 2104

Alfa AF: 0.311 Hom.: 4237

Bravo AF: 0.343

Asia WGS AF: 0.500 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17042288; hg19: chr2-657954;