rs368182

Positions:

• chr16-62988576-A-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 0.224 in 152,082 control chromosomes in the GnomAD database, including 3,902 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 0.22 (3902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) 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: 0.224 AC: 34041 AN: 151964 Hom.: 3901 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.224 AC: 34061 AN: 152082 Hom.: 3902 Cov.: 32 AF XY: 0.225 AC XY: 16697 AN XY: 74362

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.216

Alfa AF: 0.230 Hom.: 697

Bravo AF: 0.229

Asia WGS AF: 0.211 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs368182; hg19: chr16-63022480;