rs1413753

chr6-130829364-T-Cchr6-130829364-T-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+1713T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,112 control chromosomes in the GnomAD database, including 36,437 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 0.69 (36437 hom., cov: 32)
• Consequence: SMLR1 NM_001195597.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMLR1	NM_001195597.2	c.238+1713T>C		intron_variant		ENST00000541421.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMLR1	ENST00000541421.2	c.238+1713T>C		intron_variant		1	NM_001195597.2	P1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104856 AN: 151994 Hom.: 36413 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.690 AC: 104926 AN: 152112 Hom.: 36437 Cov.: 32 AF XY: 0.698 AC XY: 51931 AN XY: 74368

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.655

Alfa AF: 0.686 Hom.: 4437

Bravo AF: 0.674

Asia WGS AF: 0.774 AC: 2690 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.2
Dann	Benign	0.84

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: rs1413753; hg19: chr6-131150504;