rs547709819

Variant names:

• chr11-107630448-T-C
• NM_018712.4:c.49T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-107630448-T-C
• chr11-107630448-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018712.4(ELMOD1):​c.49T>C​(p.Cys17Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,450,844 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: ELMOD1 NM_018712.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.49

Genes affected

ELMOD1 (HGNC:25334): (ELMO domain containing 1) Enables GTPase activator activity. Predicted to be involved in positive regulation of GTPase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMOD1	NM_018712.4	c.49T>C	p.Cys17Arg	missense_variant	Exon 3 of 12	ENST00000265840.12	NP_061182.3
ELMOD1	NM_001308018.2	c.31T>C	p.Cys11Arg	missense_variant	Exon 4 of 13		NP_001294947.1
ELMOD1	NM_001130037.2	c.49T>C	p.Cys17Arg	missense_variant	Exon 3 of 11		NP_001123509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMOD1	ENST00000265840.12	c.49T>C	p.Cys17Arg	missense_variant	Exon 3 of 12	1	NM_018712.4	ENSP00000265840.7
ELMOD1	ENST00000531234.5	c.31T>C	p.Cys11Arg	missense_variant	Exon 4 of 13	2		ENSP00000433232.1
ELMOD1	ENST00000443271.2	c.49T>C	p.Cys17Arg	missense_variant	Exon 3 of 11	2		ENSP00000412257.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.89e-7 AC: 1 AN: 1450844 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 720290

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000189

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.58
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.29
CADD	Benign	22
DANN	Uncertain	0.97
DEOGEN2	Benign	0.035	T;T;.
Eigen	Benign	0.031
Eigen_PC	Uncertain	0.22
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.81	T;T;T
M_CAP	Benign	0.0055	T
MetaRNN	Uncertain	0.64	D;D;D
MetaSVM	Benign	-0.88	T
MutationAssessor	Benign	1.7	.;L;L
PrimateAI	Pathogenic	0.91	D
PROVEAN	Benign	-1.5	N;N;N
REVEL	Uncertain	0.31
Sift	Benign	0.38	T;T;T
Sift4G	Benign	0.40	T;T;T
Polyphen		0.012	.;B;.
Vest4		0.93
MutPred		0.58		.;Gain of MoRF binding (P = 0.0394);Gain of MoRF binding (P = 0.0394);
MVP		0.15
MPC		0.65
ClinPred		0.91	D
GERP RS		5.5
Varity_R		0.60
gMVP		0.77

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-107501174;