16-56958105-G-A

Variant names:

• chr16-56958105-G-A
• rs6499863

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.265 AC: 10886 AN: 41068

American (AMR) AF: 0.147 AC: 2238 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 491 AN: 3466

East Asian (EAS) AF: 0.122 AC: 631 AN: 5152

South Asian (SAS) AF: 0.0893 AC: 427 AN: 4782

European-Finnish (FIN) AF: 0.119 AC: 1226 AN: 10300

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11116 AN: 67874

Other (OTH) AF: 0.183 AC: 382 AN: 2090

Alfa AF: 0.174 Hom.: 6904

Bravo AF: 0.191

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.43
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6499863; hg19: chr16-56992017;