6-130829486-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195597.2(SMLR1):c.238+1835A>G 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 152,090 control chromosomes in the GnomAD database, including 11,194 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 (11194 hom., cov: 32)
• Consequence: SMLR1 NM_001195597.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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/exons	MANE	UniProt
SMLR1	NM_001195597.2	c.238+1835A>G		intron_variant		ENST00000541421.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMLR1	ENST00000541421.2	c.238+1835A>G		intron_variant		1	NM_001195597.2	P1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56514 AN: 151972 Hom.: 11179 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.372 AC: 56568 AN: 152090 Hom.: 11194 Cov.: 32 AF XY: 0.381 AC XY: 28299 AN XY: 74322

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.351

Alfa AF: 0.325 Hom.: 1035

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	-0.88
Cadd	Benign	0.78
Dann	Benign	0.34

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

Other links and lift over

dbSNP: rs1413754; hg19: chr6-131150626;