Variant chr6-130827723-A-T 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.238+72A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 1,093,996 control chromosomes in the GnomAD database, including 64,874 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 ( 11136 hom., cov: 31)

Exomes 𝑓: 0.32 ( 53738 hom. )

Consequence

SMLR1
NM_001195597.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.231

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 (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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.238+72A>T		intron_variant		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.238+72A>T		intron_variant		1	NM_001195597.2	ENSP00000456026	P1

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56373

AN:

151792

Hom.:

11121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.432

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.647

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.320

AC:

301044

AN:

942086

Hom.:

53738

AF XY:

0.324

AC XY:

155887

AN XY:

480496

show subpopulations

Gnomad4 AFR exome

AF:

0.424

Gnomad4 AMR exome

AF:

0.498

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.644

Gnomad4 SAS exome

AF:

0.473

Gnomad4 FIN exome

AF:

0.405

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.334

GnomAD4 genome

AF:

0.371

AC:

56427

AN:

151910

Hom.:

11136

Cov.:

AF XY:

0.380

AC XY:

28229

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.436

Gnomad4 ASJ

AF:

0.230

Gnomad4 EAS

AF:

0.648

Gnomad4 SAS

AF:

0.488

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.292

Gnomad4 OTH

AF:

0.352

Alfa

AF:

0.336

Hom.:

1120

Bravo

AF:

0.376

Asia WGS

AF:

0.576

AC:

2000

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.6

DANN

Benign

0.44

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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