rs9388856

Variant names:

• chr6-130827723-A-T
• rs9388856
• NM_001195597.2:c.238+72A>T

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+72A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 1,093,996 control chromosomes in the GnomAD database, including 64,874 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 (11136 hom., cov: 31)
  • Exomes 𝑓: 0.32 (53738 hom.)
• Consequence: SMLR1 NM_001195597.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 9 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=-0.84).
• 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+72A>T		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+72A>T		intron_variant	Intron 1 of 1	1	NM_001195597.2	ENSP00000456026.1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56373 AN: 151792 Hom.: 11121 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.436

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: 0.349

GnomAD4 exome AF: 0.320 AC: 301044 AN: 942086 Hom.: 53738 AF XY: 0.324 AC XY: 155887 AN XY: 480496

African (AFR) AF: 0.424 AC: 9460 AN: 22328

American (AMR) AF: 0.498 AC: 16781 AN: 33666

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 4849 AN: 21530

East Asian (EAS) AF: 0.644 AC: 21475 AN: 33326

South Asian (SAS) AF: 0.473 AC: 31904 AN: 67500

European-Finnish (FIN) AF: 0.405 AC: 13401 AN: 33088

Middle Eastern (MID) AF: 0.246 AC: 1157 AN: 4702

European-Non Finnish (NFE) AF: 0.275 AC: 187672 AN: 683038

Other (OTH) AF: 0.334 AC: 14345 AN: 42908

GnomAD4 genome AF: 0.371 AC: 56427 AN: 151910 Hom.: 11136 Cov.: 31 AF XY: 0.380 AC XY: 28229 AN XY: 74230

African (AFR) AF: 0.432 AC: 17876 AN: 41394

American (AMR) AF: 0.436 AC: 6664 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3468

East Asian (EAS) AF: 0.648 AC: 3339 AN: 5156

South Asian (SAS) AF: 0.488 AC: 2342 AN: 4802

European-Finnish (FIN) AF: 0.421 AC: 4438 AN: 10544

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

European-Non Finnish (NFE) AF: 0.292 AC: 19862 AN: 67958

Other (OTH) AF: 0.352 AC: 742 AN: 2110

Alfa AF: 0.336 Hom.: 1120

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	-0.84
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		0.23
PromoterAI		0.019	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs9388856; hg19: chr6-131148863;