chr7-37375454-G-A

Variant names:

• chr7-37375454-G-A
• rs9969311
• NM_014800.11:c.-73-32691C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014800.11(ELMO1):​c.-73-32691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 655,996 control chromosomes in the GnomAD database, including 16,901 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 0.18 (3011 hom., cov: 32)
  • Exomes 𝑓: 0.19 (13890 hom.)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 8 publications found

Genes affected

ELMO1 (HGNC:16286): (engulfment and cell motility 1) This gene encodes a member of the engulfment and cell motility protein family. These proteins interact with dedicator of cytokinesis proteins to promote phagocytosis and cell migration. Increased expression of this gene and dedicator of cytokinesis 1 may promote glioma cell invasion, and single nucleotide polymorphisms in this gene may be associated with diabetic nephropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

RPS10P14 (HGNC:35880): (ribosomal protein S10 pseudogene 14)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014800.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	NM_014800.11	MANE Select	c.-73-32691C>T		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.-73-32691C>T		intron	N/A	NP_001193409.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.-73-32691C>T		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.-73-32691C>T		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000453399.5	TSL:5	c.-74+18368C>T		intron	N/A	ENSP00000391734.1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26750 AN: 151964 Hom.: 3003 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.193 AC: 97131 AN: 503914 Hom.: 13890 AF XY: 0.197 AC XY: 52988 AN XY: 268924

African (AFR) AF: 0.174 AC: 2543 AN: 14612

American (AMR) AF: 0.333 AC: 10067 AN: 30274

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 2208 AN: 16240

East Asian (EAS) AF: 0.605 AC: 18965 AN: 31322

South Asian (SAS) AF: 0.305 AC: 16219 AN: 53216

European-Finnish (FIN) AF: 0.171 AC: 5433 AN: 31746

Middle Eastern (MID) AF: 0.194 AC: 412 AN: 2124

European-Non Finnish (NFE) AF: 0.122 AC: 36295 AN: 296342

Other (OTH) AF: 0.178 AC: 4989 AN: 28038

GnomAD4 genome AF: 0.176 AC: 26788 AN: 152082 Hom.: 3011 Cov.: 32 AF XY: 0.185 AC XY: 13742 AN XY: 74328

African (AFR) AF: 0.176 AC: 7317 AN: 41502

American (AMR) AF: 0.248 AC: 3797 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3468

East Asian (EAS) AF: 0.587 AC: 3029 AN: 5158

South Asian (SAS) AF: 0.295 AC: 1414 AN: 4794

European-Finnish (FIN) AF: 0.173 AC: 1829 AN: 10586

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8335 AN: 67972

Other (OTH) AF: 0.189 AC: 398 AN: 2108

Alfa AF: 0.0975 Hom.: 207

Bravo AF: 0.185

Asia WGS AF: 0.406 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.56
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9969311; hg19: chr7-37415057;