2-21160845-C-T

Variant names:

• chr2-21160845-C-T
• rs4560142

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 152,100 control chromosomes in the GnomAD database, including 44,188 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 (44188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 15 publications found

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 = 0.971 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: 114931 AN: 151982 Hom.: 44156 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.756 AC: 115016 AN: 152100 Hom.: 44188 Cov.: 32 AF XY: 0.759 AC XY: 56400 AN XY: 74346

African (AFR) AF: 0.623 AC: 25842 AN: 41450

American (AMR) AF: 0.808 AC: 12356 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3468

East Asian (EAS) AF: 0.994 AC: 5135 AN: 5166

South Asian (SAS) AF: 0.854 AC: 4123 AN: 4826

European-Finnish (FIN) AF: 0.763 AC: 8062 AN: 10568

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

European-Non Finnish (NFE) AF: 0.800 AC: 54407 AN: 68014

Other (OTH) AF: 0.757 AC: 1600 AN: 2114

Alfa AF: 0.783 Hom.: 136306

Bravo AF: 0.753

Asia WGS AF: 0.917 AC: 3187 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	0.44
DANN	Benign	0.16
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4560142; hg19: chr2-21383717;