6-130828738-T-G

Variant names:

• chr6-130828738-T-G
• rs9388857
• NM_001195597.2:c.238+1087T>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+1087T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,980 control chromosomes in the GnomAD database, including 11,148 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 (11148 hom., cov: 32)
• Consequence: SMLR1 NM_001195597.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.935
• 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=-0.59).
• 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 rank	MANE	Protein	UniProt
SMLR1	NM_001195597.2	c.238+1087T>G		intron_variant	Intron 1 of 1	ENST00000541421.2	NP_001182526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMLR1	ENST00000541421.2	c.238+1087T>G		intron_variant	Intron 1 of 1	1	NM_001195597.2	ENSP00000456026.1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56388 AN: 151862 Hom.: 11133 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.437

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: 0.348

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

GnomAD4 genome AF: 0.371 AC: 56442 AN: 151980 Hom.: 11148 Cov.: 32 AF XY: 0.380 AC XY: 28246 AN XY: 74290

African (AFR) AF: 0.432 AC: 17889 AN: 41416

American (AMR) AF: 0.437 AC: 6668 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 795 AN: 3464

East Asian (EAS) AF: 0.647 AC: 3343 AN: 5166

South Asian (SAS) AF: 0.488 AC: 2354 AN: 4824

European-Finnish (FIN) AF: 0.421 AC: 4445 AN: 10558

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.292 AC: 19843 AN: 67966

Other (OTH) AF: 0.351 AC: 741 AN: 2114

Alfa AF: 0.349 Hom.: 1733

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	-0.59
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		0.94

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: rs9388857; hg19: chr6-131149878;