rs30882

Variant names:

• chr16-62965569-T-C
• rs30882

Your query was ambiguous. Multiple possible variants found:

• chr16-62965569-T-C
• chr16-62965569-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 152,148 control chromosomes in the GnomAD database, including 2,709 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 (2709 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 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: 0.178 AC: 27071 AN: 152030 Hom.: 2708 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.178 AC: 27080 AN: 152148 Hom.: 2709 Cov.: 32 AF XY: 0.179 AC XY: 13305 AN XY: 74388

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.181

Alfa AF: 0.202 Hom.: 3127

Bravo AF: 0.178

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30882; hg19: chr16-62999473;