2-127818257-C-T

Variant names:

• chr2-127818257-C-T
• rs2109312

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 0.127 in 151,772 control chromosomes in the GnomAD database, including 1,518 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 0.13 (1518 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 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: 0.127 AC: 19315 AN: 151676 Hom.: 1515 Cov.: 31

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.127 AC: 19345 AN: 151772 Hom.: 1518 Cov.: 31 AF XY: 0.128 AC XY: 9509 AN XY: 74148

African (AFR) AF: 0.0679 AC: 2810 AN: 41368

American (AMR) AF: 0.143 AC: 2178 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3470

East Asian (EAS) AF: 0.143 AC: 736 AN: 5158

South Asian (SAS) AF: 0.282 AC: 1353 AN: 4790

European-Finnish (FIN) AF: 0.110 AC: 1158 AN: 10480

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9767 AN: 67964

Other (OTH) AF: 0.150 AC: 316 AN: 2100

Alfa AF: 0.0645 Hom.: 68

Bravo AF: 0.124

Asia WGS AF: 0.215 AC: 747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.54
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2109312; hg19: chr2-128575831;