chr19-51987997-A-G

Position:

• chr19-51987997-A-G

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 0.193 in 152,066 control chromosomes in the GnomAD database, including 3,299 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 0.19 (3299 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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: 0.193 AC: 29333 AN: 151948 Hom.: 3286 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.0743

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.193 AC: 29386 AN: 152066 Hom.: 3299 Cov.: 31 AF XY: 0.195 AC XY: 14533 AN XY: 74344

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.0749

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.206

Alfa AF: 0.145 Hom.: 2268

Bravo AF: 0.198

Asia WGS AF: 0.219 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8112515; hg19: chr19-52491250;