rs11767398

Positions:

• chr7-112489954-A-C
• chr7-112489954-A-T

Variant summary

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

The NM_182597.3(LSMEM1):​c.*5A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,610,028 control chromosomes in the GnomAD database, including 237,784 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 0.45 (17645 hom., cov: 32)
  • Exomes 𝑓: 0.54 (220139 hom.)
• Consequence: LSMEM1 NM_182597.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946

Genes affected

LSMEM1 (HGNC:22036): (leucine rich single-pass membrane protein 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000288640 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LSMEM1	NM_182597.3	c.*5A>C		3_prime_UTR_variant	4/4	ENST00000312849.4	NP_872403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSMEM1	ENST00000312849.4	c.*5A>C		3_prime_UTR_variant	4/4	1	NM_182597.3	ENSP00000323304.3
ENSG00000288640	ENST00000676282.1	n.*563A>C		non_coding_transcript_exon_variant	15/15			ENSP00000501830.1
ENSG00000288640	ENST00000676282.1	n.*563A>C		3_prime_UTR_variant	15/15			ENSP00000501830.1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68562 AN: 151942 Hom.: 17653 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.495

GnomAD3 exomes AF: 0.461 AC: 114358 AN: 247828 Hom.: 30429 AF XY: 0.473 AC XY: 63450 AN XY: 134026

Gnomad AFR exome AF: 0.241

Gnomad AMR exome AF: 0.252

Gnomad ASJ exome AF: 0.632

Gnomad EAS exome AF: 0.169

Gnomad SAS exome AF: 0.335

Gnomad FIN exome AF: 0.630

Gnomad NFE exome AF: 0.588

Gnomad OTH exome AF: 0.511

GnomAD4 exome AF: 0.536 AC: 781402 AN: 1457970 Hom.: 220139 Cov.: 39 AF XY: 0.533 AC XY: 386656 AN XY: 725322

Gnomad4 AFR exome AF: 0.234

Gnomad4 AMR exome AF: 0.265

Gnomad4 ASJ exome AF: 0.631

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.340

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.580

Gnomad4 OTH exome AF: 0.514

GnomAD4 genome AF: 0.451 AC: 68568 AN: 152058 Hom.: 17645 Cov.: 32 AF XY: 0.449 AC XY: 33390 AN XY: 74344

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.494

Alfa AF: 0.552 Hom.: 26046

Bravo AF: 0.423

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.46

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: rs11767398; hg19: chr7-112130009; COSMIC: COSV57196151;