chr2-21166787-T-G

Variant names:

• chr2-21166787-T-G
• rs4635554

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 0.372 in 151,354 control chromosomes in the GnomAD database, including 10,930 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 0.37 (10930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658
• Publications: 25 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 (AFR) allele frequency at 95% confidence interval = 0.481 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: 0.372 AC: 56188 AN: 151234 Hom.: 10897 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.372 AC: 56275 AN: 151354 Hom.: 10930 Cov.: 32 AF XY: 0.367 AC XY: 27184 AN XY: 73988

African (AFR) AF: 0.487 AC: 20152 AN: 41404

American (AMR) AF: 0.344 AC: 5243 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 909 AN: 3456

East Asian (EAS) AF: 0.402 AC: 2070 AN: 5154

South Asian (SAS) AF: 0.247 AC: 1188 AN: 4814

European-Finnish (FIN) AF: 0.268 AC: 2827 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22636 AN: 67430

Other (OTH) AF: 0.354 AC: 746 AN: 2106

Alfa AF: 0.362 Hom.: 9784

Bravo AF: 0.386

Asia WGS AF: 0.343 AC: 1179 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.6
DANN	Benign	0.87
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs4635554; hg19: chr2-21389659;