5-1446274-A-G

Variant names:

• chr5-1446274-A-G
• rs2652511

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 0.505 in 152,014 control chromosomes in the GnomAD database, including 20,422 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 0.50 (20422 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• Publications: 58 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 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: 0.505 AC: 76686 AN: 151896 Hom.: 20401 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.505 AC: 76765 AN: 152014 Hom.: 20422 Cov.: 33 AF XY: 0.504 AC XY: 37452 AN XY: 74308

African (AFR) AF: 0.376 AC: 15573 AN: 41468

American (AMR) AF: 0.481 AC: 7350 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3466

East Asian (EAS) AF: 0.171 AC: 879 AN: 5154

South Asian (SAS) AF: 0.507 AC: 2445 AN: 4822

European-Finnish (FIN) AF: 0.561 AC: 5935 AN: 10576

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40673 AN: 67932

Other (OTH) AF: 0.525 AC: 1105 AN: 2106

Alfa AF: 0.554 Hom.: 10233

Bravo AF: 0.489

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.44
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2652511; hg19: chr5-1446389;