rs5024431

Variant names:

• chr6-32716567-G-A
• rs5024431

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 0.321 in 152,014 control chromosomes in the GnomAD database, including 8,880 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 0.32 (8880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48676 AN: 151896 Hom.: 8863 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.321 AC: 48749 AN: 152014 Hom.: 8880 Cov.: 32 AF XY: 0.316 AC XY: 23515 AN XY: 74304

African (AFR) AF: 0.493 AC: 20407 AN: 41418

American (AMR) AF: 0.308 AC: 4710 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1574 AN: 5176

South Asian (SAS) AF: 0.303 AC: 1455 AN: 4808

European-Finnish (FIN) AF: 0.185 AC: 1960 AN: 10572

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16267 AN: 67980

Other (OTH) AF: 0.346 AC: 728 AN: 2106

Alfa AF: 0.285 Hom.: 19789

Bravo AF: 0.342

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.88
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs5024431; hg19: chr6-32684344;