rs1994417

chr19-43683354-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;