rs1338623

chr1-205420750-C-G

Variant summary

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

The NM_001199050.2(LEMD1):c.-38-176G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 152,288 control chromosomes in the GnomAD database, including 102 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 0.026 (102 hom., cov: 32)
• Consequence: LEMD1 NM_001199050.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

Genes affected

LEMD1 (HGNC:18725): (LEM domain containing 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LEMD1	NM_001199050.2	c.-38-176G>C		intron_variant		ENST00000367153.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LEMD1	ENST00000367153.9	c.-38-176G>C		intron_variant		1	NM_001199050.2	P2
LEMD1	ENST00000476884.1	n.42-176G>C		intron_variant, non_coding_transcript_variant		1
LEMD1	ENST00000367154.5	c.-38-176G>C		intron_variant		2		A2
LEMD1	ENST00000495594.2	c.-38-176G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0262 AC: 3988 AN: 152170 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.00827

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00648

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0262 AC: 3993 AN: 152288 Hom.: 102 Cov.: 32 AF XY: 0.0278 AC XY: 2067 AN XY: 74456

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.0119

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.00925

Gnomad4 SAS AF: 0.00828

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.00648

Gnomad4 OTH AF: 0.0176

Alfa AF: 0.0183 Hom.: 9

Bravo AF: 0.0257

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	11
Dann	Benign	0.69

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: rs1338623; hg19: chr1-205389878;