rs4286803

chr6-144209396-T-C

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 0.505 in 152,076 control chromosomes in the GnomAD database, including 20,897 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 0.50 (20897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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: 0.505 AC: 76671 AN: 151958 Hom.: 20849 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.505 AC: 76771 AN: 152076 Hom.: 20897 Cov.: 32 AF XY: 0.506 AC XY: 37642 AN XY: 74348

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.495

Alfa AF: 0.421 Hom.: 28831

Bravo AF: 0.523

Asia WGS AF: 0.664 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.7
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4286803; hg19: chr6-144530533; COSMIC: COSV69429403;