19-50861124-C-T

Variant names:

• chr19-50861124-C-T
• rs8104556

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 0.169 in 152,154 control chromosomes in the GnomAD database, including 2,316 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 0.17 (2316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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: 0.169 AC: 25652 AN: 152036 Hom.: 2316 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.169 AC: 25671 AN: 152154 Hom.: 2316 Cov.: 32 AF XY: 0.163 AC XY: 12109 AN XY: 74388

African (AFR) AF: 0.220 AC: 9140 AN: 41466

American (AMR) AF: 0.118 AC: 1807 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.0286 AC: 148 AN: 5178

South Asian (SAS) AF: 0.137 AC: 663 AN: 4828

European-Finnish (FIN) AF: 0.0895 AC: 949 AN: 10606

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11896 AN: 67996

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.162 Hom.: 1767

Bravo AF: 0.172

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.59
PhyloP100		1.1
PromoterAI		-0.012	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8104556; hg19: chr19-51364380;