rs1922713

Variant names:

• chr2-129194000-A-C
• rs1922713

Your query was ambiguous. Multiple possible variants found:

• chr2-129194000-A-C
• chr2-129194000-A-G

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 0.0213 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0299 AC: 1243 AN: 41560

American (AMR) AF: 0.0103 AC: 158 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3470

East Asian (EAS) AF: 0.0383 AC: 198 AN: 5166

South Asian (SAS) AF: 0.0768 AC: 370 AN: 4816

European-Finnish (FIN) AF: 0.0685 AC: 726 AN: 10600

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00647 AC: 440 AN: 68030

Other (OTH) AF: 0.0161 AC: 34 AN: 2116

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
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs1922713; hg19: chr2-129951573;