chr19-54136764-C-T

Variant names:

• chr19-54136764-C-T
• rs36643

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 0.573 in 152,128 control chromosomes in the GnomAD database, including 25,471 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 0.57 (25471 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 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: 0.573 AC: 87135 AN: 152008 Hom.: 25462 Cov.: 33

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.573 AC: 87169 AN: 152128 Hom.: 25471 Cov.: 33 AF XY: 0.575 AC XY: 42731 AN XY: 74354

African (AFR) AF: 0.451 AC: 18707 AN: 41480

American (AMR) AF: 0.628 AC: 9609 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2338 AN: 3470

East Asian (EAS) AF: 0.769 AC: 3980 AN: 5174

South Asian (SAS) AF: 0.424 AC: 2046 AN: 4824

European-Finnish (FIN) AF: 0.644 AC: 6815 AN: 10586

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41693 AN: 67984

Other (OTH) AF: 0.578 AC: 1222 AN: 2114

Alfa AF: 0.602 Hom.: 54858

Bravo AF: 0.570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.6
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs36643; hg19: chr19-54640480;