19-51987997-A-G

Variant names:

• chr19-51987997-A-G
• rs8112515

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 0.193 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
• Publications: 8 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.308 AC: 12749 AN: 41432

American (AMR) AF: 0.146 AC: 2231 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3468

East Asian (EAS) AF: 0.0749 AC: 388 AN: 5180

South Asian (SAS) AF: 0.285 AC: 1374 AN: 4814

European-Finnish (FIN) AF: 0.160 AC: 1690 AN: 10576

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9458 AN: 67984

Other (OTH) AF: 0.206 AC: 435 AN: 2116

Alfa AF: 0.148 Hom.: 2820

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8112515; hg19: chr19-52491250;