rs56131196

Positions:

• chr19-44919589-G-A

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 0.179 in 152,130 control chromosomes in the GnomAD database, including 2,537 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 0.18 (2537 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27108 AN: 152012 Hom.: 2528 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.179 AC: 27161 AN: 152130 Hom.: 2537 Cov.: 31 AF XY: 0.185 AC XY: 13729 AN XY: 74354

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.140

Alfa AF: 0.174 Hom.: 460

Bravo AF: 0.166

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56131196; hg19: chr19-45422846;