rs1369330

Positions:

• chr2-220977972-G-A

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 0.393 in 152,034 control chromosomes in the GnomAD database, including 13,101 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 0.39 (13101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59785 AN: 151916 Hom.: 13102 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.393 AC: 59808 AN: 152034 Hom.: 13101 Cov.: 32 AF XY: 0.392 AC XY: 29148 AN XY: 74310

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.417

Alfa AF: 0.430 Hom.: 1830

Bravo AF: 0.386

Asia WGS AF: 0.423 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.20
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1369330; hg19: chr2-221842692;