2-21170751-A-G

Variant names:

• chr2-21170751-A-G
• rs576203

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 0.765 in 152,040 control chromosomes in the GnomAD database, including 45,075 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 0.77 (45075 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.765 AC: 116259 AN: 151922 Hom.: 45035 Cov.: 32

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.765 AC: 116354 AN: 152040 Hom.: 45075 Cov.: 32 AF XY: 0.767 AC XY: 57006 AN XY: 74334

African (AFR) AF: 0.657 AC: 27230 AN: 41442

American (AMR) AF: 0.809 AC: 12369 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2434 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5143 AN: 5176

South Asian (SAS) AF: 0.847 AC: 4086 AN: 4826

European-Finnish (FIN) AF: 0.763 AC: 8066 AN: 10574

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54362 AN: 67954

Other (OTH) AF: 0.761 AC: 1607 AN: 2112

Alfa AF: 0.765 Hom.: 8342

Bravo AF: 0.765

Asia WGS AF: 0.919 AC: 3191 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.82
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs576203; hg19: chr2-21393623;