rs1368064

Variant names:

• chr2-221224796-A-T
• rs1368064

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 0.226 in 151,726 control chromosomes in the GnomAD database, including 4,292 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 0.23 (4292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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: 0.226 AC: 34191 AN: 151606 Hom.: 4278 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.226 AC: 34230 AN: 151726 Hom.: 4292 Cov.: 32 AF XY: 0.224 AC XY: 16637 AN XY: 74236

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.250

Alfa AF: 0.202 Hom.: 407

Bravo AF: 0.243

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368064; hg19: chr2-222089516;