rs1364477

Positions:

• chr2-185319303-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0886

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.182

Alfa AF: 0.163 Hom.: 440

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364477; hg19: chr2-186184030;