2-20934123-A-G

Variant names:

• chr2-20934123-A-G
• rs10198175

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.933 in 152,320 control chromosomes in the GnomAD database, including 66,492 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 0.93 (66492 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.933 AC: 142034 AN: 152202 Hom.: 66429 Cov.: 34

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.954

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

GnomAD4 genome AF: 0.933 AC: 142156 AN: 152320 Hom.: 66492 Cov.: 34 AF XY: 0.934 AC XY: 69529 AN XY: 74474

African (AFR) AF: 0.981 AC: 40808 AN: 41578

American (AMR) AF: 0.944 AC: 14448 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3335 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5173 AN: 5188

South Asian (SAS) AF: 0.903 AC: 4354 AN: 4822

European-Finnish (FIN) AF: 0.920 AC: 9765 AN: 10614

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61366 AN: 68026

Other (OTH) AF: 0.955 AC: 2018 AN: 2114

Alfa AF: 0.916 Hom.: 77333

Bravo AF: 0.939

Asia WGS AF: 0.955 AC: 3321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	18
DANN	Benign	0.62
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs10198175; hg19: chr2-21133883;