rs1993104

Variant names:

• chr19-51736996-C-T
• rs1993104

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.185 AC: 7702 AN: 41532

American (AMR) AF: 0.207 AC: 3161 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5184

South Asian (SAS) AF: 0.181 AC: 871 AN: 4824

European-Finnish (FIN) AF: 0.228 AC: 2409 AN: 10588

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17308 AN: 68008

Other (OTH) AF: 0.222 AC: 470 AN: 2116

Alfa AF: 0.242 Hom.: 14259

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1993104; hg19: chr19-52240249;