19-39254056-C-T

Variant names:

• chr19-39254056-C-T
• rs16973285

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 0.0755 in 143,062 control chromosomes in the GnomAD database, including 459 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 0.076 (459 hom., cov: 25)
• Consequence: MSRB1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 2 publications found

Genes affected

MSRB1P1 (HGNC:43985): (methionine sulfoxide reductase B1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0911 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 10802 AN: 142978 Hom.: 459 Cov.: 25

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00546

Gnomad SAS AF: 0.0469

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.0755 AC: 10806 AN: 143062 Hom.: 459 Cov.: 25 AF XY: 0.0740 AC XY: 5092 AN XY: 68786

African (AFR) AF: 0.0531 AC: 2052 AN: 38626

American (AMR) AF: 0.0630 AC: 863 AN: 13702

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 532 AN: 3434

East Asian (EAS) AF: 0.00548 AC: 27 AN: 4930

South Asian (SAS) AF: 0.0473 AC: 213 AN: 4504

European-Finnish (FIN) AF: 0.0790 AC: 662 AN: 8380

Middle Eastern (MID) AF: 0.0778 AC: 21 AN: 270

European-Non Finnish (NFE) AF: 0.0931 AC: 6181 AN: 66410

Other (OTH) AF: 0.0730 AC: 140 AN: 1918

Alfa AF: 0.0892 Hom.: 1175

Bravo AF: 0.0746

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs16973285; hg19: chr19-39744696;