rs16996148

Variant names:

• chr19-19547663-G-T
• rs16996148

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 0.0993 in 152,240 control chromosomes in the GnomAD database, including 871 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 0.099 (871 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 117 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15072 AN: 152122 Hom.: 856 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0871

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0993 AC: 15117 AN: 152240 Hom.: 871 Cov.: 33 AF XY: 0.0983 AC XY: 7322 AN XY: 74450

African (AFR) AF: 0.157 AC: 6510 AN: 41518

American (AMR) AF: 0.0697 AC: 1067 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.0869 AC: 449 AN: 5168

South Asian (SAS) AF: 0.110 AC: 533 AN: 4828

European-Finnish (FIN) AF: 0.0628 AC: 667 AN: 10620

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0793 AC: 5394 AN: 68020

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.0866 Hom.: 2080

Bravo AF: 0.102

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.71
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs16996148; hg19: chr19-19658472;