rs6534639

Variant names:

• chr4-79900765-C-A
• rs6534639

Your query was ambiguous. Multiple possible variants found:

• chr4-79900765-C-A
• chr4-79900765-C-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 0.493 in 148,308 control chromosomes in the GnomAD database, including 17,829 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 0.49 (17829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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: 0.493 AC: 73035 AN: 148200 Hom.: 17822 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.493 AC: 73078 AN: 148308 Hom.: 17829 Cov.: 32 AF XY: 0.493 AC XY: 35558 AN XY: 72120

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.467

Alfa AF: 0.509 Hom.: 9452

Bravo AF: 0.471

Asia WGS AF: 0.371 AC: 1277 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
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: rs6534639; hg19: chr4-80821919;