rs16996148

Variant names:

• chr19-19547663-G-T
• rs16996148

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 0.0993 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0991 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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0697

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.0869

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0628

Gnomad4 NFE AF: 0.0793

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.0802 Hom.: 551

Bravo AF: 0.102

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16996148; hg19: chr19-19658472;