Variant 6-130834931-GT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001195597.2(SMLR1):c.301delT(p.Tyr101fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00273 in 1,535,314 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 13 hom. )

Consequence

SMLR1
NM_001195597.2 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.10

Variant links:

Genes affected

SMLR1 (HGNC:44670): (small leucine rich protein 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SMLR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 6-130834931-GT-G is Benign according to our data. Variant chr6-130834931-GT-G is described in ClinVar as [Likely_benign]. Clinvar id is 2656910.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMLR1	NM_001195597.2 linkuse as main transcript	c.301delT	p.Tyr101fs	frameshift_variant	2/2	ENST00000541421.2	NP_001182526.1	H3BR10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMLR1	ENST00000541421.2 linkuse as main transcript	c.301delT	p.Tyr101fs	frameshift_variant	2/2	1	NM_001195597.2	ENSP00000456026.1		H3BR10

Frequencies

GnomAD3 genomes

AF:

0.00237

AC:

361

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000590

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00311

Gnomad FIN

AF:

0.00791

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00345

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00212

AC:

290

AN:

136572

Hom.:

AF XY:

0.00213

AC XY:

158

AN XY:

74146

show subpopulations

Gnomad AFR exome

AF:

0.000778

Gnomad AMR exome

AF:

0.000613

Gnomad ASJ exome

AF:

0.000241

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00280

Gnomad FIN exome

AF:

0.00818

Gnomad NFE exome

AF:

0.00281

Gnomad OTH exome

AF:

0.00169

GnomAD4 exome

AF:

0.00277

AC:

3834

AN:

1383044

Hom.:

Cov.:

AF XY:

0.00284

AC XY:

1935

AN XY:

682474

show subpopulations

Gnomad4 AFR exome

AF:

0.000190

Gnomad4 AMR exome

AF:

0.000504

Gnomad4 ASJ exome

AF:

0.0000795

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.00317

Gnomad4 FIN exome

AF:

0.00788

Gnomad4 NFE exome

AF:

0.00293

Gnomad4 OTH exome

AF:

0.00223

GnomAD4 genome

AF:

0.00237

AC:

361

AN:

152270

Hom.:

Cov.:

AF XY:

0.00261

AC XY:

194

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.000589

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.00791

Gnomad4 NFE

AF:

0.00344

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00298

Hom.:

Bravo

AF:

0.00163

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

SMLR1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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