chr7-112487017-C-T

Variant names:

• chr7-112487017-C-T
• rs544127044
• NM_182597.3:c.222C>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_182597.3(LSMEM1):​c.222C>T​(p.Ser74Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LSMEM1 NM_182597.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BP7: Synonymous conserved (PhyloP=0.637 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182597.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSMEM1	NM_182597.3	MANE Select	c.222C>T	p.Ser74Ser	synonymous	Exon 3 of 4	NP_872403.1	Q8N8F7-1
	LSMEM1	NM_001134468.2		c.222C>T	p.Ser74Ser	synonymous	Exon 3 of 4	NP_001127940.1	Q8N8F7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSMEM1	ENST00000312849.4	TSL:1 MANE Select	c.222C>T	p.Ser74Ser	synonymous	Exon 3 of 4	ENSP00000323304.3	Q8N8F7-1
	ENSG00000288640	ENST00000676282.1		n.*384C>T		non_coding_transcript_exon	Exon 14 of 15	ENSP00000501830.1
	ENSG00000288640	ENST00000676282.1		n.*384C>T		3_prime_UTR	Exon 14 of 15	ENSP00000501830.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	7.4
DANN	Benign	0.66
PhyloP100		0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs544127044; hg19: chr7-112127072;