2-191168974-A-T

Variant names:

• chr2-191168974-A-T
• rs2054090

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 0.37 in 152,072 control chromosomes in the GnomAD database, including 13,323 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 0.37 (13323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.370 AC: 56163 AN: 151954 Hom.: 13280 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.370 AC: 56264 AN: 152072 Hom.: 13323 Cov.: 32 AF XY: 0.363 AC XY: 26978 AN XY: 74332

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.358

Alfa AF: 0.308 Hom.: 1171

Bravo AF: 0.389

Asia WGS AF: 0.388 AC: 1344 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.37
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: rs2054090; hg19: chr2-192033700;