rs1464338

Variant names:

• chr2-187629268-A-T
• rs1464338

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 0.0707 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.132 AC: 5471 AN: 41518

American (AMR) AF: 0.114 AC: 1740 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 90 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5172

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4822

European-Finnish (FIN) AF: 0.0182 AC: 193 AN: 10598

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0425 AC: 2893 AN: 68002

Other (OTH) AF: 0.0711 AC: 150 AN: 2110

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1464338; hg19: chr2-188493995;