rs1654514

chr19-50896788-T-C

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 0.137 in 152,140 control chromosomes in the GnomAD database, including 4,602 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 0.14 (4602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.136 AC: 20745 AN: 152022 Hom.: 4575 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00520

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.137 AC: 20826 AN: 152140 Hom.: 4602 Cov.: 32 AF XY: 0.132 AC XY: 9810 AN XY: 74386

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.0551

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.000754

Gnomad4 NFE AF: 0.00519

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0821 Hom.: 348

Bravo AF: 0.155

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.2
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1654514; hg19: chr19-51400044;