rs6862199

Variant names:

• chr5-56713185-T-C
• rs6862199

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 0.476 in 151,966 control chromosomes in the GnomAD database, including 18,254 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 0.48 (18254 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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: 0.477 AC: 72378 AN: 151848 Hom.: 18244 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.476 AC: 72408 AN: 151966 Hom.: 18254 Cov.: 31 AF XY: 0.470 AC XY: 34939 AN XY: 74280

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.501

Alfa AF: 0.552 Hom.: 34174

Bravo AF: 0.474

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6862199; hg19: chr5-56009012;