rs1348864

Variant names:

• chr2-22959390-A-C
• rs1348864

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;