rs1994417

Variant names:

• chr19-43683354-C-T
• rs1994417

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 0.312 in 152,004 control chromosomes in the GnomAD database, including 8,895 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 0.31 (8895 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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: 0.312 AC: 47343 AN: 151886 Hom.: 8887 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.312 AC: 47380 AN: 152004 Hom.: 8895 Cov.: 31 AF XY: 0.320 AC XY: 23796 AN XY: 74276

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.331

Alfa AF: 0.314 Hom.: 9106

Bravo AF: 0.322

Asia WGS AF: 0.591 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.30
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1994417; hg19: chr19-44187506;