19-50919402-T-G

Variant names:

• chr19-50919402-T-G
• rs73598979

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 0.0938 in 152,082 control chromosomes in the GnomAD database, including 1,030 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 0.094 (1030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 2 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 = 0.194 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: 0.0937 AC: 14237 AN: 151964 Hom.: 1025 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0865

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0938 AC: 14270 AN: 152082 Hom.: 1030 Cov.: 31 AF XY: 0.0948 AC XY: 7049 AN XY: 74356

African (AFR) AF: 0.197 AC: 8175 AN: 41452

American (AMR) AF: 0.0865 AC: 1321 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.0856 AC: 440 AN: 5142

South Asian (SAS) AF: 0.0475 AC: 229 AN: 4816

European-Finnish (FIN) AF: 0.0658 AC: 698 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0468 AC: 3182 AN: 68006

Other (OTH) AF: 0.0735 AC: 155 AN: 2110

Alfa AF: 0.0990 Hom.: 468

Bravo AF: 0.101

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.76
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs73598979; hg19: chr19-51422658;