Variant rs1044303 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001195597.2(SMLR1):c.184G>A(p.Val62Met) variant causes a missense change. The variant allele was found at a frequency of 0.33 in 1,535,464 control chromosomes in the GnomAD database, including 89,532 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 0.37 ( 11134 hom., cov: 31)

Exomes 𝑓: 0.33 ( 78398 hom. )

Consequence

SMLR1
NM_001195597.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.53

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.7580086E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMLR1	NM_001195597.2 linkuse as main transcript	c.184G>A	p.Val62Met	missense_variant	1/2	ENST00000541421.2	NP_001182526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMLR1	ENST00000541421.2 linkuse as main transcript	c.184G>A	p.Val62Met	missense_variant	1/2	1	NM_001195597.2	ENSP00000456026	P1

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56306

AN:

151648

Hom.:

11119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.432

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.650

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.347

GnomAD3 exomes

AF:

0.397

AC:

54294

AN:

136896

Hom.:

12004

AF XY:

0.394

AC XY:

29315

AN XY:

74332

show subpopulations

Gnomad AFR exome

AF:

0.440

Gnomad AMR exome

AF:

0.516

Gnomad ASJ exome

AF:

0.231

Gnomad EAS exome

AF:

0.644

Gnomad SAS exome

AF:

0.479

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.285

Gnomad OTH exome

AF:

0.341

GnomAD4 exome

AF:

0.326

AC:

450885

AN:

1383698

Hom.:

78398

Cov.:

AF XY:

0.329

AC XY:

224372

AN XY:

682798

show subpopulations

Gnomad4 AFR exome

AF:

0.437

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.646

Gnomad4 SAS exome

AF:

0.478

Gnomad4 FIN exome

AF:

0.406

Gnomad4 NFE exome

AF:

0.294

Gnomad4 OTH exome

AF:

0.344

GnomAD4 genome

AF:

0.371

AC:

56360

AN:

151766

Hom.:

11134

Cov.:

AF XY:

0.380

AC XY:

28185

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.436

Gnomad4 ASJ

AF:

0.230

Gnomad4 EAS

AF:

0.650

Gnomad4 SAS

AF:

0.487

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.292

Gnomad4 OTH

AF:

0.350

Alfa

AF:

0.303

Hom.:

11598

Bravo

AF:

0.376

TwinsUK

AF:

0.308

AC:

1142

ALSPAC

AF:

0.292

AC:

1126

ExAC

AF:

0.337

AC:

5946

Asia WGS

AF:

0.576

AC:

1999

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.27

CADD

Uncertain

DANN

Benign

0.97

DEOGEN2

Benign

0.076

FATHMM_MKL

Uncertain

0.95

LIST_S2

Benign

0.69

MetaRNN

Benign

0.0000068

MutationAssessor

Benign

0.81

PrimateAI

Uncertain

0.60

PROVEAN

Uncertain

-3.0

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Vest4

0.15

GERP RS

5.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.28

gMVP

0.12

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over