Genetic Variant SMLR1:c.238+625C>T (chr6-130828276-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001195597.2(SMLR1):c.238+625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,952 control chromosomes in the GnomAD database, including 11,157 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 ( 11157 hom., cov: 32)

Consequence

SMLR1
NM_001195597.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.183

Publications

7 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMLR1	NM_001195597.2 link	c.238+625C>T		intron_variant	Intron 1 of 1	ENST00000541421.2	NP_001182526.1	H3BR10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMLR1	ENST00000541421.2 link	c.238+625C>T		intron_variant	Intron 1 of 1	1	NM_001195597.2	ENSP00000456026.1		H3BR10

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56422

AN:

151834

Hom.:

11142

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:

0.649

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.423

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.346

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

GnomAD4 genome

AF:

0.372

AC:

56476

AN:

151952

Hom.:

11157

Cov.:

AF XY:

0.381

AC XY:

28259

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.432

AC:

17905

AN:

41442

American (AMR)

AF:

0.436

AC:

6656

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

796

AN:

3468

East Asian (EAS)

AF:

0.649

AC:

3362

AN:

5180

South Asian (SAS)

AF:

0.490

AC:

2349

AN:

4798

European-Finnish (FIN)

AF:

0.423

AC:

4452

AN:

10534

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.292

AC:

19853

AN:

67960

Other (OTH)

AF:

0.349

AC:

737

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1759

3518

5278

7037

8796

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.349

Hom.:

1739

Bravo

AF:

0.376

Asia WGS

AF:

0.576

AC:

2001

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.4

(source)

DANN

Benign

0.51

PhyloP100

0.18

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

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6-130828276-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over