2-21161810-A-G

Variant names:

• chr2-21161810-A-G
• rs547235

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 0.755 in 151,410 control chromosomes in the GnomAD database, including 43,856 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 (43856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 0.755 AC: 114248 AN: 151292 Hom.: 43824 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.800

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.755 AC: 114333 AN: 151410 Hom.: 43856 Cov.: 32 AF XY: 0.758 AC XY: 56045 AN XY: 73978

African (AFR) AF: 0.622 AC: 25642 AN: 41258

American (AMR) AF: 0.807 AC: 12299 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2424 AN: 3460

East Asian (EAS) AF: 0.994 AC: 5074 AN: 5106

South Asian (SAS) AF: 0.854 AC: 4114 AN: 4818

European-Finnish (FIN) AF: 0.762 AC: 8026 AN: 10532

Middle Eastern (MID) AF: 0.792 AC: 228 AN: 288

European-Non Finnish (NFE) AF: 0.799 AC: 54119 AN: 67704

Other (OTH) AF: 0.757 AC: 1594 AN: 2106

Alfa AF: 0.255 Hom.: 2391

Bravo AF: 0.753

Asia WGS AF: 0.915 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.8
DANN	Benign	0.58
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs547235; hg19: chr2-21384682;