2-185319303-A-G

Variant names:

• chr2-185319303-A-G
• rs1364477

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 0.162 in 152,078 control chromosomes in the GnomAD database, including 2,300 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 0.16 (2300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 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: 0.162 AC: 24688 AN: 151960 Hom.: 2297 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.162 AC: 24694 AN: 152078 Hom.: 2300 Cov.: 32 AF XY: 0.168 AC XY: 12476 AN XY: 74338

African (AFR) AF: 0.0886 AC: 3678 AN: 41510

American (AMR) AF: 0.265 AC: 4041 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1632 AN: 5162

South Asian (SAS) AF: 0.127 AC: 614 AN: 4816

European-Finnish (FIN) AF: 0.231 AC: 2446 AN: 10578

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11303 AN: 67982

Other (OTH) AF: 0.182 AC: 385 AN: 2110

Alfa AF: 0.165 Hom.: 3356

Bravo AF: 0.165

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.8
DANN	Benign	0.81
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1364477; hg19: chr2-186184030;