19-5841345-G-T

Variant names:

• chr19-5841345-G-T
• rs3760775

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 0.154 in 152,204 control chromosomes in the GnomAD database, including 2,613 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 0.15 (2613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.154 AC: 23356 AN: 152086 Hom.: 2599 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0615

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.154 AC: 23405 AN: 152204 Hom.: 2613 Cov.: 32 AF XY: 0.159 AC XY: 11845 AN XY: 74406

African (AFR) AF: 0.270 AC: 11201 AN: 41532

American (AMR) AF: 0.235 AC: 3591 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1624 AN: 5156

South Asian (SAS) AF: 0.192 AC: 927 AN: 4828

European-Finnish (FIN) AF: 0.116 AC: 1230 AN: 10604

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

European-Non Finnish (NFE) AF: 0.0615 AC: 4184 AN: 67998

Other (OTH) AF: 0.150 AC: 317 AN: 2110

Alfa AF: 0.0960 Hom.: 3040

Bravo AF: 0.166

Asia WGS AF: 0.331 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs3760775; hg19: chr19-5841356;