chr11-107630453-A-G

Variant names:

• chr11-107630453-A-G
• rs35291603
• NM_018712.4:c.54A>G

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_018712.4(ELMOD1):​c.54A>G​(p.Lys18Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00222 in 1,603,900 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0013 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0023 (6 hom.)
• Consequence: ELMOD1 NM_018712.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.209
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 11-107630453-A-G is Benign according to our data. Variant chr11-107630453-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2642355.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 6 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018712.4. 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
	ELMOD1	NM_018712.4	MANE Select	c.54A>G	p.Lys18Lys	synonymous	Exon 3 of 12	NP_061182.3
	ELMOD1	NM_001308018.2		c.36A>G	p.Lys12Lys	synonymous	Exon 4 of 13	NP_001294947.1	E9PLM8
	ELMOD1	NM_001130037.2		c.54A>G	p.Lys18Lys	synonymous	Exon 3 of 11	NP_001123509.1	Q8N336-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMOD1	ENST00000265840.12	TSL:1 MANE Select	c.54A>G	p.Lys18Lys	synonymous	Exon 3 of 12	ENSP00000265840.7	Q8N336-1
	ELMOD1	ENST00000531234.5	TSL:2	c.36A>G	p.Lys12Lys	synonymous	Exon 4 of 13	ENSP00000433232.1	E9PLM8
	ELMOD1	ENST00000443271.2	TSL:2	c.54A>G	p.Lys18Lys	synonymous	Exon 3 of 11	ENSP00000412257.2	Q8N336-3

Frequencies

GnomAD3 genomes AF: 0.00128 AC: 194 AN: 152028 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000266

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000378

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00257

Gnomad OTH AF: 0.00144

GnomAD2 exomes AF: 0.00114 AC: 264 AN: 232466 AF XY: 0.000990

Gnomad AFR exome AF: 0.000277

Gnomad AMR exome AF: 0.0000922

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000288

Gnomad NFE exome AF: 0.00238

Gnomad OTH exome AF: 0.000525

GnomAD4 exome AF: 0.00232 AC: 3373 AN: 1451754 Hom.: 6 Cov.: 32 AF XY: 0.00219 AC XY: 1582 AN XY: 720844

African (AFR) AF: 0.000269 AC: 9 AN: 33406

American (AMR) AF: 0.0000927 AC: 4 AN: 43148

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25900

East Asian (EAS) AF: 0.00 AC: 0 AN: 39482

South Asian (SAS) AF: 0.00 AC: 0 AN: 84242

European-Finnish (FIN) AF: 0.000302 AC: 16 AN: 52930

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5756

European-Non Finnish (NFE) AF: 0.00296 AC: 3279 AN: 1106834

Other (OTH) AF: 0.00108 AC: 65 AN: 60056

GnomAD4 genome AF: 0.00128 AC: 194 AN: 152146 Hom.: 1 Cov.: 32 AF XY: 0.00118 AC XY: 88 AN XY: 74374

African (AFR) AF: 0.000265 AC: 11 AN: 41490

American (AMR) AF: 0.0000654 AC: 1 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.000378 AC: 4 AN: 10584

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00257 AC: 175 AN: 68016

Other (OTH) AF: 0.00142 AC: 3 AN: 2106

Alfa AF: 0.00233 Hom.: 0

Bravo AF: 0.00123

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.60
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.38		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.38		Position offset: 1

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs35291603; hg19: chr11-107501179;