chr2-36822420-A-T

Variant names:

• chr2-36822420-A-T
• rs888053

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 0.474 in 152,116 control chromosomes in the GnomAD database, including 17,544 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 0.47 (17544 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.474 AC: 72022 AN: 151998 Hom.: 17507 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.474 AC: 72109 AN: 152116 Hom.: 17544 Cov.: 33 AF XY: 0.477 AC XY: 35517 AN XY: 74384

African (AFR) AF: 0.521 AC: 21602 AN: 41488

American (AMR) AF: 0.523 AC: 8000 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3464

East Asian (EAS) AF: 0.748 AC: 3880 AN: 5184

South Asian (SAS) AF: 0.584 AC: 2814 AN: 4820

European-Finnish (FIN) AF: 0.414 AC: 4382 AN: 10580

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28582 AN: 67978

Other (OTH) AF: 0.463 AC: 978 AN: 2114

Alfa AF: 0.302 Hom.: 823

Bravo AF: 0.484

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0030
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs888053; hg19: chr2-37049563;