rs16879736

Variant names:

• chr6-87713447-C-T
• rs16879736

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 0.106 in 151,942 control chromosomes in the GnomAD database, including 945 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 0.11 (945 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 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: 0.106 AC: 16123 AN: 151826 Hom.: 944 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0820

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.106 AC: 16135 AN: 151942 Hom.: 945 Cov.: 31 AF XY: 0.107 AC XY: 7943 AN XY: 74262

African (AFR) AF: 0.105 AC: 4370 AN: 41452

American (AMR) AF: 0.126 AC: 1917 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0820 AC: 284 AN: 3464

East Asian (EAS) AF: 0.193 AC: 1000 AN: 5184

South Asian (SAS) AF: 0.118 AC: 566 AN: 4814

European-Finnish (FIN) AF: 0.102 AC: 1069 AN: 10496

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0966 AC: 6566 AN: 67964

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.0994 Hom.: 692

Bravo AF: 0.111

Asia WGS AF: 0.154 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs16879736; hg19: chr6-88423165;