chr2-19352628-T-C

Position:

• chr2-19352628-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_145260.3(OSR1):​c.666-218A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,114 control chromosomes in the GnomAD database, including 60,209 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.89 (60209 hom., cov: 30)
• Consequence: OSR1 NM_145260.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.36

Genes affected

OSR1 (HGNC:8111): (odd-skipped related transcription factor 1) Enables sequence-specific double-stranded DNA binding activity. Involved in negative regulation of ion transmembrane transporter activity; positive regulation of gastrulation; and pronephros development. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 2-19352628-T-C is Benign according to our data. Variant chr2-19352628-T-C is described in ClinVar as [Benign]. Clinvar id is 1231818.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OSR1	NM_145260.3	c.666-218A>G		intron_variant		ENST00000272223.3	NP_660303.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OSR1	ENST00000272223.3	c.666-218A>G		intron_variant		1	NM_145260.3	ENSP00000272223.2
OSR1	ENST00000487581.1	n.3773-218A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135005 AN: 151996 Hom.: 60166 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.888 AC: 135101 AN: 152114 Hom.: 60209 Cov.: 30 AF XY: 0.890 AC XY: 66200 AN XY: 74364

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.892

Alfa AF: 0.899 Hom.: 80452

Bravo AF: 0.886

Asia WGS AF: 0.932 AC: 3244 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs851066; hg19: chr2-19552389;