19-57349717-T-C

Position:

• chr19-57349717-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 0.64 in 152,086 control chromosomes in the GnomAD database, including 31,521 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 0.64 (31521 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57349717T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97299 AN: 151968 Hom.: 31478 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.640 AC: 97386 AN: 152086 Hom.: 31521 Cov.: 32 AF XY: 0.639 AC XY: 47541 AN XY: 74342

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.600

Alfa AF: 0.627 Hom.: 17346

Bravo AF: 0.640

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7250371; hg19: chr19-57861085;