2-138787007-C-T

Variant names:

• chr2-138787007-C-T
• rs4954956

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 0.252 in 152,052 control chromosomes in the GnomAD database, including 4,820 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 0.25 (4820 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.278 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: 0.252 AC: 38247 AN: 151932 Hom.: 4815 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.252 AC: 38268 AN: 152052 Hom.: 4820 Cov.: 33 AF XY: 0.249 AC XY: 18536 AN XY: 74300

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.264

Alfa AF: 0.253 Hom.: 2700

Bravo AF: 0.261

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4954956; hg19: chr2-139544577;