rs4286803

Variant names:

• chr6-144209396-T-C
• rs4286803

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;