rs6599400

chr4-1783298-A-Cchr4-1783298-A-Gchr4-1783298-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 0.649 in 151,036 control chromosomes in the GnomAD database, including 32,679 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 (32679 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 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: 0.650 AC: 98022 AN: 150918 Hom.: 32658 Cov.: 26

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.649 AC: 98084 AN: 151036 Hom.: 32679 Cov.: 26 AF XY: 0.662 AC XY: 48781 AN XY: 73742

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.640

Alfa AF: 0.637 Hom.: 36777

Bravo AF: 0.631

Asia WGS AF: 0.821 AC: 2854 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.80
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6599400; hg19: chr4-1785025;