rs1464338

chr2-187629268-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 0.0707 in 152,176 control chromosomes in the GnomAD database, including 550 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 0.071 (550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0707 AC: 10751 AN: 152058 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0707 AC: 10766 AN: 152176 Hom.: 550 Cov.: 32 AF XY: 0.0698 AC XY: 5193 AN XY: 74396

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0260

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.0182

Gnomad4 NFE AF: 0.0425

Gnomad4 OTH AF: 0.0711

Alfa AF: 0.0564 Hom.: 48

Bravo AF: 0.0807

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.22
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1464338; hg19: chr2-188493995;