chr2-85356880-CA-C

Position:

• chr2-85356880-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001135022.2(ELMOD3):​c.-232-72del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0030 (0 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ELMOD3 NM_001135022.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.706

Genes affected

ELMOD3 (HGNC:26158): (ELMO domain containing 3) This gene encodes a member of the engulfment and cell motility family of GTPase-activating proteins that regulate Arf GTPase proteins. Members of this family are defined by a conserved engulfment and cell motility domain. In rat cochlea, the encoded protein is found in stereocilia, kinocilia and cuticular plate of developing hair cells suggesting a function for this protein in cochlear sensory cells. An allelic variant of this family has been associated with autosomal recessive nonsyndromic deafness-88 in humans. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-85356880-CA-C is Benign according to our data. Variant chr2-85356880-CA-C is described in ClinVar as [Likely_benign]. Clinvar id is 1316665.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMOD3	NM_001135022.2	c.-232-72del		intron_variant		ENST00000409013.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMOD3	ENST00000409013.8	c.-232-72del		intron_variant		1	NM_001135022.2	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 374 AN: 124800 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00472

Gnomad ASJ AF: 0.00164

Gnomad EAS AF: 0.00338

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.00397

Gnomad NFE AF: 0.00235

Gnomad OTH AF: 0.00357

GnomAD4 exome AF: 0.199 AC: 2919 AN: 14668 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 1522 AN XY: 7594

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.189

Gnomad4 ASJ exome AF: 0.197

Gnomad4 EAS exome AF: 0.197

Gnomad4 SAS exome AF: 0.198

Gnomad4 FIN exome AF: 0.184

Gnomad4 NFE exome AF: 0.201

Gnomad4 OTH exome AF: 0.210

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00303 AC: 378 AN: 124818 Hom.: 0 Cov.: 32 AF XY: 0.00321 AC XY: 192 AN XY: 59858

Gnomad4 AFR AF: 0.00140

Gnomad4 AMR AF: 0.00472

Gnomad4 ASJ AF: 0.00164

Gnomad4 EAS AF: 0.00340

Gnomad4 SAS AF: 0.00150

Gnomad4 FIN AF: 0.0148

Gnomad4 NFE AF: 0.00235

Gnomad4 OTH AF: 0.00413

Alfa AF: 0.0000644 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs759699457; hg19: chr2-85584003;