22-29232752-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133455.4(EMID1):c.823+350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 222,688 control chromosomes in the GnomAD database, including 13,922 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 0.30 (8653 hom., cov: 33)
  • Exomes 𝑓: 0.36 (5269 hom.)
• Consequence: EMID1 NM_133455.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.81

Genes affected

EMID1 (HGNC:18036): (EMI domain containing 1) Predicted to be located in several cellular components, including Golgi apparatus; endoplasmic reticulum; and extracellular matrix. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EMID1	NM_133455.4	c.823+350C>T		intron_variant		ENST00000334018.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EMID1	ENST00000334018.11	c.823+350C>T		intron_variant		1	NM_133455.4	P4

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45370 AN: 152006 Hom.: 8651 Cov.: 33

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.0638

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.362 AC: 25548 AN: 70564 Hom.: 5269 Cov.: 0 AF XY: 0.360 AC XY: 13084 AN XY: 36300

Gnomad4 AFR exome AF: 0.0913

Gnomad4 AMR exome AF: 0.366

Gnomad4 ASJ exome AF: 0.505

Gnomad4 EAS exome AF: 0.0435

Gnomad4 SAS exome AF: 0.180

Gnomad4 FIN exome AF: 0.302

Gnomad4 NFE exome AF: 0.413

Gnomad4 OTH exome AF: 0.388

GnomAD4 genome AF: 0.298 AC: 45364 AN: 152124 Hom.: 8653 Cov.: 33 AF XY: 0.292 AC XY: 21673 AN XY: 74346

Gnomad4 AFR AF: 0.0868

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.0641

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.361

Alfa AF: 0.402 Hom.: 18186

Bravo AF: 0.300

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.84
Dann	Benign	0.65

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: rs1997719; hg19: chr22-29628741;