chr16-30471173-T-C

Variant names:

• chr16-30471173-T-C
• rs11150589

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 65 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.193 AC: 7985 AN: 41448

American (AMR) AF: 0.618 AC: 9391 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4997 AN: 5182

South Asian (SAS) AF: 0.757 AC: 3647 AN: 4820

European-Finnish (FIN) AF: 0.553 AC: 5806 AN: 10496

Middle Eastern (MID) AF: 0.593 AC: 172 AN: 290

European-Non Finnish (NFE) AF: 0.521 AC: 35394 AN: 67922

Other (OTH) AF: 0.529 AC: 1114 AN: 2106

Alfa AF: 0.504 Hom.: 52034

Bravo AF: 0.461

Asia WGS AF: 0.809 AC: 2807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.0
DANN	Benign	0.93
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs11150589; hg19: chr16-30482494;