chr16-19402664-C-T

Variant names:

• chr16-19402664-C-T
• rs1023446

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 0.584 in 151,922 control chromosomes in the GnomAD database, including 26,270 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 0.58 (26270 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 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: 0.584 AC: 88646 AN: 151804 Hom.: 26248 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.584 AC: 88709 AN: 151922 Hom.: 26270 Cov.: 31 AF XY: 0.585 AC XY: 43427 AN XY: 74244

African (AFR) AF: 0.510 AC: 21099 AN: 41400

American (AMR) AF: 0.631 AC: 9629 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1901 AN: 3470

East Asian (EAS) AF: 0.578 AC: 2973 AN: 5148

South Asian (SAS) AF: 0.720 AC: 3464 AN: 4812

European-Finnish (FIN) AF: 0.582 AC: 6142 AN: 10552

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41497 AN: 67958

Other (OTH) AF: 0.572 AC: 1210 AN: 2116

Alfa AF: 0.577 Hom.: 4907

Bravo AF: 0.580

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.44
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1023446; hg19: chr16-19413986;