19-39254506-C-G

Variant names:

• chr19-39254506-C-G
• rs10853728

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 0.685 in 152,010 control chromosomes in the GnomAD database, including 36,454 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 0.68 (36454 hom., cov: 31)
• Consequence: MSRB1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 29 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104029 AN: 151890 Hom.: 36429 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.685 AC: 104104 AN: 152010 Hom.: 36454 Cov.: 31 AF XY: 0.680 AC XY: 50552 AN XY: 74300

African (AFR) AF: 0.740 AC: 30688 AN: 41450

American (AMR) AF: 0.651 AC: 9941 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2409 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1054 AN: 5164

South Asian (SAS) AF: 0.510 AC: 2449 AN: 4804

European-Finnish (FIN) AF: 0.725 AC: 7667 AN: 10576

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47625 AN: 67964

Other (OTH) AF: 0.688 AC: 1447 AN: 2104

Alfa AF: 0.636 Hom.: 2101

Bravo AF: 0.682

Asia WGS AF: 0.400 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.83
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10853728; hg19: chr19-39745146;