rs1993104

Variant names:

• chr19-51736996-C-T
• rs1993104

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 0.219 in 152,218 control chromosomes in the GnomAD database, including 3,924 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 0.22 (3924 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.219 AC: 33312 AN: 152100 Hom.: 3924 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.219 AC: 33319 AN: 152218 Hom.: 3924 Cov.: 33 AF XY: 0.217 AC XY: 16163 AN XY: 74410

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.222

Alfa AF: 0.247 Hom.: 9573

Bravo AF: 0.217

Asia WGS AF: 0.0870 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993104; hg19: chr19-52240249;