chr19-44835236-T-C

Position:

• chr19-44835236-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 0.686 in 151,650 control chromosomes in the GnomAD database, including 35,923 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 0.69 (35923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.765 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: 0.686 AC: 103897 AN: 151538 Hom.: 35888 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.686 AC: 103974 AN: 151650 Hom.: 35923 Cov.: 32 AF XY: 0.688 AC XY: 50964 AN XY: 74074

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.688

Alfa AF: 0.696 Hom.: 4563

Bravo AF: 0.687

Asia WGS AF: 0.529 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4605275; hg19: chr19-45338493;