chr17-19900934-T-C

Position:

• chr17-19900934-T-C

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 0.405 in 151,892 control chromosomes in the GnomAD database, including 12,877 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 0.40 (12877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61398 AN: 151774 Hom.: 12863 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.405 AC: 61466 AN: 151892 Hom.: 12877 Cov.: 32 AF XY: 0.402 AC XY: 29829 AN XY: 74218

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.391

Alfa AF: 0.382 Hom.: 22914

Bravo AF: 0.417

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
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: rs397969; hg19: chr17-19804247;