rs6450839

chr5-31383795-A-Gchr5-31383795-A-T

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 0.646 in 152,062 control chromosomes in the GnomAD database, including 32,360 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 0.65 (32360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98125 AN: 151944 Hom.: 32330 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.646 AC: 98204 AN: 152062 Hom.: 32360 Cov.: 32 AF XY: 0.646 AC XY: 48011 AN XY: 74334

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.652

Alfa AF: 0.677 Hom.: 19158

Bravo AF: 0.647

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6450839; hg19: chr5-31383902;