rs6534639

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;