rs1368065

Variant names:

• chr2-221224808-T-C
• rs1368065

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 0.239 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.316 AC: 13102 AN: 41440

American (AMR) AF: 0.302 AC: 4610 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2044 AN: 5176

South Asian (SAS) AF: 0.342 AC: 1651 AN: 4824

European-Finnish (FIN) AF: 0.0733 AC: 777 AN: 10598

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12581 AN: 67702

Other (OTH) AF: 0.261 AC: 551 AN: 2108

Alfa AF: 0.214 Hom.: 1063

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1368065; hg19: chr2-222089528;