rs6450839

Variant names:

• chr5-31383795-A-G
• rs6450839

Your query was ambiguous. Multiple possible variants found:

• chr5-31383795-A-G
• chr5-31383795-A-T

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 0.646 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.531 AC: 22012 AN: 41472

American (AMR) AF: 0.751 AC: 11482 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2747 AN: 5172

South Asian (SAS) AF: 0.569 AC: 2743 AN: 4818

European-Finnish (FIN) AF: 0.713 AC: 7535 AN: 10566

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47429 AN: 67958

Other (OTH) AF: 0.652 AC: 1375 AN: 2108

Alfa AF: 0.676 Hom.: 21077

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6450839; hg19: chr5-31383902;