rs6499863

Positions:

• chr16-56958105-G-A

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 0.183 in 151,156 control chromosomes in the GnomAD database, including 2,778 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 0.18 (2778 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.183 AC: 27606 AN: 151066 Hom.: 2770 Cov.: 30

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.183 AC: 27636 AN: 151156 Hom.: 2778 Cov.: 30 AF XY: 0.178 AC XY: 13166 AN XY: 73798

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.183

Alfa AF: 0.169 Hom.: 3901

Bravo AF: 0.191

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6499863; hg19: chr16-56992017;