2-129194000-A-C

Position:

• chr2-129194000-A-C

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 0.0213 in 152,266 control chromosomes in the GnomAD database, including 70 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 0.021 (70 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3232 AN: 152148 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00647

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0213 AC: 3237 AN: 152266 Hom.: 70 Cov.: 32 AF XY: 0.0257 AC XY: 1912 AN XY: 74442

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.0768

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.00647

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00602 Hom.: 0

Bravo AF: 0.0165

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1922713; hg19: chr2-129951573;