rs1654514

Variant names:

• chr19-50896788-T-C
• rs1654514

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;