4-112645135-T-C

Position:

• chr4-112645135-T-C

Variant summary

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

The NM_016648.4(LARP7):​c.202+264T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,334 control chromosomes in the GnomAD database, including 35,667 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.68 (35667 hom., cov: 27)
• Consequence: LARP7 NM_016648.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.22

Genes affected

LARP7 (HGNC:24912): (La ribonucleoprotein 7, transcriptional regulator) This gene encodes a protein which is found in the 7SK snRNP (small nuclear ribonucleoprotein). This snRNP complex inhibits a cyclin-dependent kinase, positive transcription elongation factor b, which is required for paused RNA polymerase II at a promoter to begin transcription elongation. A pseudogene of this gene is located on chromosome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

LARP7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BP6: Variant 4-112645135-T-C is Benign according to our data. Variant chr4-112645135-T-C is described in ClinVar as [Benign]. Clinvar id is 1273157.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LARP7	NM_016648.4	c.202+264T>C		intron_variant		ENST00000344442.10	NP_057732.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LARP7	ENST00000344442.10	c.202+264T>C		intron_variant		2	NM_016648.4	ENSP00000344950.5

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103143 AN: 151216 Hom.: 35626 Cov.: 27

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.682 AC: 103247 AN: 151334 Hom.: 35667 Cov.: 27 AF XY: 0.686 AC XY: 50717 AN XY: 73894

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.686

Alfa AF: 0.653 Hom.: 4054

Bravo AF: 0.691

Asia WGS AF: 0.884 AC: 3073 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	-1.1
CADD	Benign	1.6
DANN	Benign	0.25

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: rs12650431; hg19: chr4-113566291;