chr2-21155933-A-G

Variant names:

• chr2-21155933-A-G
• rs312985

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 0.756 in 151,920 control chromosomes in the GnomAD database, including 44,124 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 0.76 (44124 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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: 0.756 AC: 114771 AN: 151802 Hom.: 44092 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.756 AC: 114856 AN: 151920 Hom.: 44124 Cov.: 31 AF XY: 0.759 AC XY: 56323 AN XY: 74246

African (AFR) AF: 0.623 AC: 25799 AN: 41424

American (AMR) AF: 0.808 AC: 12337 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2430 AN: 3466

East Asian (EAS) AF: 0.994 AC: 5131 AN: 5162

South Asian (SAS) AF: 0.856 AC: 4133 AN: 4830

European-Finnish (FIN) AF: 0.763 AC: 8040 AN: 10534

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

European-Non Finnish (NFE) AF: 0.800 AC: 54332 AN: 67916

Other (OTH) AF: 0.756 AC: 1597 AN: 2112

Alfa AF: 0.784 Hom.: 92475

Bravo AF: 0.753

Asia WGS AF: 0.917 AC: 3188 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.64
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs312985; hg19: chr2-21378805;