chr2-20998527-T-G

Variant names:

• chr2-20998527-T-G
• rs952275

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 0.38 in 152,014 control chromosomes in the GnomAD database, including 12,419 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 0.38 (12419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 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: 0.380 AC: 57730 AN: 151896 Hom.: 12420 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.337

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.380 AC: 57735 AN: 152014 Hom.: 12419 Cov.: 32 AF XY: 0.371 AC XY: 27565 AN XY: 74278

African (AFR) AF: 0.222 AC: 9212 AN: 41492

American (AMR) AF: 0.417 AC: 6369 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3468

East Asian (EAS) AF: 0.0502 AC: 260 AN: 5180

South Asian (SAS) AF: 0.262 AC: 1259 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4073 AN: 10554

Middle Eastern (MID) AF: 0.334 AC: 97 AN: 290

European-Non Finnish (NFE) AF: 0.500 AC: 33972 AN: 67918

Other (OTH) AF: 0.369 AC: 776 AN: 2102

Alfa AF: 0.455 Hom.: 27203

Bravo AF: 0.374

Asia WGS AF: 0.171 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.41
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs952275; hg19: chr2-21221399;