Variant 19-6415866-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001366299.1(KHSRP):c.1629A>C(p.Pro543=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000631 in 1,548,870 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00068 ( 0 hom., cov: 34)

Exomes 𝑓: 0.00063 ( 1 hom. )

Consequence

KHSRP
NM_001366299.1 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.811

Variant links:

Genes affected

KHSRP (HGNC:6316): (KH-type splicing regulatory protein) The KHSRP gene encodes a multifunctional RNA-binding protein implicated in a variety of cellular processes, including transcription, alternative pre-mRNA splicing, and mRNA localization (Min et al., 1997 [PubMed 9136930]; Gherzi et al., 2004 [PubMed 15175153]).[supplied by OMIM, Apr 2010]

KHSRP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 19-6415866-T-G is Benign according to our data. Variant chr19-6415866-T-G is described in ClinVar as [Benign]. Clinvar id is 774952.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.811 with no splicing effect.

BS2

High AC in GnomAd4 at 103 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
KHSRP	NM_001366299.1 linkuse as main transcript	c.1629A>C	p.Pro543=	synonymous_variant	16/19	ENST00000600480.2	NP_001353228.1
KHSRP	NM_003685.3 linkuse as main transcript	c.1629A>C	p.Pro543=	synonymous_variant	16/20		NP_003676.2
KHSRP	NM_001366300.1 linkuse as main transcript	c.1629A>C	p.Pro543=	synonymous_variant	16/20		NP_001353229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
KHSRP	ENST00000600480.2 linkuse as main transcript	c.1629A>C	p.Pro543=	synonymous_variant	16/19	2	NM_001366299.1	ENSP00000471146	A2
KHSRP	ENST00000398148.7 linkuse as main transcript	c.1629A>C	p.Pro543=	synonymous_variant	16/20	1		ENSP00000381216	P2
KHSRP	ENST00000595223.5 linkuse as main transcript	c.378A>C	p.Pro126=	synonymous_variant	4/8	5		ENSP00000473254

Frequencies

GnomAD3 genomes

AF:

0.000684

AC:

103

AN:

150684

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000171

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000791

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000210

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00120

Gnomad OTH

AF:

0.000487

GnomAD3 exomes

AF:

0.000413

AC:

AN:

169534

Hom.:

AF XY:

0.000414

AC XY:

AN XY:

91770

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000328

Gnomad ASJ exome

AF:

0.000505

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000485

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000778

Gnomad OTH exome

AF:

0.000233

GnomAD4 exome

AF:

0.000626

AC:

875

AN:

1398070

Hom.:

Cov.:

AF XY:

0.000648

AC XY:

446

AN XY:

688798

show subpopulations

Gnomad4 AFR exome

AF:

0.0000312

Gnomad4 AMR exome

AF:

0.000511

Gnomad4 ASJ exome

AF:

0.000742

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000515

Gnomad4 FIN exome

AF:

0.0000204

Gnomad4 NFE exome

AF:

0.000748

Gnomad4 OTH exome

AF:

0.000416

GnomAD4 genome

AF:

0.000683

AC:

103

AN:

150800

Hom.:

Cov.:

AF XY:

0.000570

AC XY:

AN XY:

73632

show subpopulations

Gnomad4 AFR

AF:

0.000171

Gnomad4 AMR

AF:

0.000790

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000211

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00120

Gnomad4 OTH

AF:

0.000482

Alfa

AF:

0.000427

Hom.:

Bravo

AF:

0.000748

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

6.6

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over