19-7564594-C-T

Position:

• chr19-7564594-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 0.448 in 151,974 control chromosomes in the GnomAD database, including 15,927 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 0.45 (15927 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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: 0.448 AC: 67968 AN: 151856 Hom.: 15905 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.448 AC: 68035 AN: 151974 Hom.: 15927 Cov.: 31 AF XY: 0.447 AC XY: 33193 AN XY: 74260

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.479

Alfa AF: 0.412 Hom.: 1587

Bravo AF: 0.454

Asia WGS AF: 0.555 AC: 1929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs542419; hg19: chr19-7629480;