chr2-20981153-G-T

Variant names:

• chr2-20981153-G-T
• rs6544366

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 0.242 in 152,094 control chromosomes in the GnomAD database, including 5,507 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 0.24 (5507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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: 0.242 AC: 36757 AN: 151974 Hom.: 5508 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.242 AC: 36752 AN: 152094 Hom.: 5507 Cov.: 32 AF XY: 0.249 AC XY: 18525 AN XY: 74354

African (AFR) AF: 0.149 AC: 6183 AN: 41504

American (AMR) AF: 0.230 AC: 3518 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3741 AN: 5154

South Asian (SAS) AF: 0.533 AC: 2559 AN: 4804

European-Finnish (FIN) AF: 0.272 AC: 2878 AN: 10582

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16088 AN: 67982

Other (OTH) AF: 0.246 AC: 518 AN: 2108

Alfa AF: 0.253 Hom.: 11844

Bravo AF: 0.233

Asia WGS AF: 0.586 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.32
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6544366; hg19: chr2-21204025;