rs6499861

Variant names:

• chr16-56957583-C-G
• rs6499861

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 0.176 in 151,874 control chromosomes in the GnomAD database, including 2,598 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 (2598 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 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: 0.176 AC: 26683 AN: 151756 Hom.: 2591 Cov.: 30

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.176 AC: 26712 AN: 151874 Hom.: 2598 Cov.: 30 AF XY: 0.172 AC XY: 12756 AN XY: 74212

African (AFR) AF: 0.257 AC: 10633 AN: 41374

American (AMR) AF: 0.140 AC: 2137 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3468

East Asian (EAS) AF: 0.105 AC: 542 AN: 5162

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4818

European-Finnish (FIN) AF: 0.119 AC: 1255 AN: 10540

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10721 AN: 67948

Other (OTH) AF: 0.175 AC: 369 AN: 2104

Alfa AF: 0.175 Hom.: 294

Bravo AF: 0.184

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.64
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs6499861; hg19: chr16-56991495;