2-20985339-A-G

Variant names:

• chr2-20985339-A-G
• rs7557067

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 0.241 in 152,110 control chromosomes in the GnomAD database, including 5,453 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 (5453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 52 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 (EAS) allele frequency at 95% confidence interval = 0.694 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: 36708 AN: 151992 Hom.: 5455 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: 0.713

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.241 AC: 36702 AN: 152110 Hom.: 5453 Cov.: 32 AF XY: 0.249 AC XY: 18492 AN XY: 74336

African (AFR) AF: 0.149 AC: 6173 AN: 41520

American (AMR) AF: 0.229 AC: 3504 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3674 AN: 5152

South Asian (SAS) AF: 0.533 AC: 2569 AN: 4816

European-Finnish (FIN) AF: 0.272 AC: 2880 AN: 10576

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

European-Non Finnish (NFE) AF: 0.237 AC: 16115 AN: 67986

Other (OTH) AF: 0.247 AC: 521 AN: 2110

Alfa AF: 0.243 Hom.: 9307

Bravo AF: 0.232

Asia WGS AF: 0.581 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.44
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs7557067; hg19: chr2-21208211;