16-30471173-T-C

Position:

• chr16-30471173-T-C

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 0.467 in 151,834 control chromosomes in the GnomAD database, including 19,474 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 0.47 (19474 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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: 0.467 AC: 70871 AN: 151716 Hom.: 19465 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.467 AC: 70882 AN: 151834 Hom.: 19474 Cov.: 30 AF XY: 0.478 AC XY: 35417 AN XY: 74166

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.529

Alfa AF: 0.513 Hom.: 18792

Bravo AF: 0.461

Asia WGS AF: 0.809 AC: 2807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.0
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11150589; hg19: chr16-30482494;