chr19-47890785-G-T

Variant names:

• chr19-47890785-G-T
• rs2910400

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 0.69 in 151,962 control chromosomes in the GnomAD database, including 36,252 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 0.69 (36252 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.690 AC: 104758 AN: 151844 Hom.: 36218 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.690 AC: 104848 AN: 151962 Hom.: 36252 Cov.: 31 AF XY: 0.690 AC XY: 51242 AN XY: 74286

African (AFR) AF: 0.691 AC: 28652 AN: 41436

American (AMR) AF: 0.695 AC: 10585 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3468

East Asian (EAS) AF: 0.764 AC: 3952 AN: 5170

South Asian (SAS) AF: 0.736 AC: 3544 AN: 4816

European-Finnish (FIN) AF: 0.666 AC: 7039 AN: 10564

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46962 AN: 67964

Other (OTH) AF: 0.649 AC: 1369 AN: 2110

Alfa AF: 0.685 Hom.: 159841

Bravo AF: 0.690

Asia WGS AF: 0.731 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.26
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2910400; hg19: chr19-48394042;