rs16996148

chr19-19547663-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;