19-7564594-C-T

Variant names:

• chr19-7564594-C-T
• rs542419

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.554 AC: 22970 AN: 41454

American (AMR) AF: 0.373 AC: 5688 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1485 AN: 3468

East Asian (EAS) AF: 0.674 AC: 3468 AN: 5148

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4810

European-Finnish (FIN) AF: 0.383 AC: 4045 AN: 10560

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27197 AN: 67968

Other (OTH) AF: 0.479 AC: 1012 AN: 2112

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs542419; hg19: chr19-7629480;