rs16879736

chr6-87713447-C-T

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 0.106 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0820

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0993 Hom.: 586

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16879736; hg19: chr6-88423165;