NM_001195597.2:c.238+1835A>G

Variant names:

• chr6-130829486-A-G
• rs1413754
• NM_001195597.2:c.238+1835A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195597.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMLR1	NM_001195597.2	MANE Select	c.238+1835A>G		intron	N/A	NP_001182526.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMLR1	ENST00000541421.2	TSL:1 MANE Select	c.238+1835A>G		intron	N/A	ENSP00000456026.1

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

African (AFR) AF: 0.433 AC: 17953 AN: 41482

American (AMR) AF: 0.437 AC: 6670 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3355 AN: 5164

South Asian (SAS) AF: 0.489 AC: 2353 AN: 4816

European-Finnish (FIN) AF: 0.421 AC: 4456 AN: 10578

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19873 AN: 67984

Other (OTH) AF: 0.351 AC: 742 AN: 2112

Alfa AF: 0.329 Hom.: 1107

Bravo AF: 0.376

Asia WGS AF: 0.576 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.78
DANN	Benign	0.34
PhyloP100		-0.35

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

Other links and lift over

dbSNP: rs1413754; hg19: chr6-131150626;