rs2107369

Positions:

• chr16-68082115-T-G

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 0.178 in 152,072 control chromosomes in the GnomAD database, including 2,729 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 (2729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27007 AN: 151954 Hom.: 2716 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.178 AC: 27055 AN: 152072 Hom.: 2729 Cov.: 32 AF XY: 0.181 AC XY: 13438 AN XY: 74348

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0806

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.179

Alfa AF: 0.162 Hom.: 450

Bravo AF: 0.179

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2107369; hg19: chr16-68116018;