rs5024431

Variant names:

• chr6-32716567-G-A
• rs5024431

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 0.321 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.320 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

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.346

Alfa AF: 0.261 Hom.: 8552

Bravo AF: 0.342

Asia WGS AF: 0.265 AC: 920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5024431; hg19: chr6-32684344;