rs1348864

Positions:

• chr2-22959390-A-C
• chr2-22959390-A-T

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 0.668 in 152,028 control chromosomes in the GnomAD database, including 34,215 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 0.67 (34215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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: 0.667 AC: 101397 AN: 151910 Hom.: 34173 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.668 AC: 101490 AN: 152028 Hom.: 34215 Cov.: 32 AF XY: 0.665 AC XY: 49393 AN XY: 74288

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.657

Alfa AF: 0.663 Hom.: 64150

Bravo AF: 0.657

Asia WGS AF: 0.500 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1348864; hg19: chr2-23182262;