rs1368065

Variant names:

• chr2-221224808-T-C
• rs1368065

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 0.239 in 151,686 control chromosomes in the GnomAD database, including 4,907 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 (4907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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: 0.239 AC: 36231 AN: 151568 Hom.: 4891 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36274 AN: 151686 Hom.: 4907 Cov.: 32 AF XY: 0.238 AC XY: 17663 AN XY: 74200

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.261

Alfa AF: 0.207 Hom.: 877

Bravo AF: 0.258

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368065; hg19: chr2-222089528;