11-107631613-G-T

Variant names:

• chr11-107631613-G-T
• NM_018712.4:c.226G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_018712.4(ELMOD1):​c.226G>T​(p.Ala76Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000707 in 1,413,560 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: ELMOD1 NM_018712.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15106133).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMOD1	NM_018712.4	c.226G>T	p.Ala76Ser	missense_variant	Exon 5 of 12	ENST00000265840.12	NP_061182.3
ELMOD1	NM_001308018.2	c.208G>T	p.Ala70Ser	missense_variant	Exon 6 of 13		NP_001294947.1
ELMOD1	NM_001130037.2	c.226G>T	p.Ala76Ser	missense_variant	Exon 5 of 11		NP_001123509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMOD1	ENST00000265840.12	c.226G>T	p.Ala76Ser	missense_variant	Exon 5 of 12	1	NM_018712.4	ENSP00000265840.7
ELMOD1	ENST00000531234.5	c.208G>T	p.Ala70Ser	missense_variant	Exon 6 of 13	2		ENSP00000433232.1
ELMOD1	ENST00000443271.2	c.226G>T	p.Ala76Ser	missense_variant	Exon 5 of 11	2		ENSP00000412257.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.07e-7 AC: 1 AN: 1413560 Hom.: 0 Cov.: 29 AF XY: 0.00000143 AC XY: 1 AN XY: 698616

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: 0.00

Gnomad4 NFE exome AF: 9.20e-7

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	Benign	0.085
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	17
DANN	Benign	0.65
DEOGEN2	Benign	0.0041	T;T;.
Eigen	Benign	-0.24
Eigen_PC	Benign	-0.031
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.88	D;D;D
M_CAP	Benign	0.0059	T
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	0.90	.;L;L
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	-0.21	N;N;N
REVEL	Benign	0.066
Sift	Benign	0.65	T;T;T
Sift4G	Benign	0.72	T;T;T
Polyphen		0.011	.;B;.
Vest4		0.21
MutPred		0.29		.;Gain of disorder (P = 0.032);Gain of disorder (P = 0.032);
MVP		0.093
MPC		0.089
ClinPred		0.62	D
GERP RS		5.7
Varity_R		0.053
gMVP		0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: chr11-107502339;