5-123321505-G-A

Variant names:

• chr5-123321505-G-A
• rs1582931

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 0.512 in 152,020 control chromosomes in the GnomAD database, including 20,032 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 0.51 (20032 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77806 AN: 151900 Hom.: 20001 Cov.: 33

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.512 AC: 77899 AN: 152020 Hom.: 20032 Cov.: 33 AF XY: 0.515 AC XY: 38303 AN XY: 74322

African (AFR) AF: 0.553 AC: 22940 AN: 41486

American (AMR) AF: 0.522 AC: 7978 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1510 AN: 3460

East Asian (EAS) AF: 0.588 AC: 3034 AN: 5162

South Asian (SAS) AF: 0.609 AC: 2940 AN: 4826

European-Finnish (FIN) AF: 0.515 AC: 5416 AN: 10524

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32439 AN: 67972

Other (OTH) AF: 0.538 AC: 1138 AN: 2116

Alfa AF: 0.475 Hom.: 8985

Bravo AF: 0.512

Asia WGS AF: 0.634 AC: 2198 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.32
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1582931; hg19: chr5-122657199;