22-29232752-C-T

Variant names:

• chr22-29232752-C-T
• rs1997719
• ENST00000473933.1:n.1071C>T

Variant summary

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

The ENST00000473933.1(EMID1):​n.1071C>T variant causes a non coding transcript exon 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 ENST00000473933.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.81
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000473933.1. 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
	EMID1	NM_133455.4	MANE Select	c.823+350C>T		intron	N/A	NP_597712.2
	EMID1	NM_001410828.1		c.823+350C>T		intron	N/A	NP_001397757.1
	EMID1	NM_001267895.2		c.817+350C>T		intron	N/A	NP_001254824.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMID1	ENST00000473933.1	TSL:1	n.1071C>T		non_coding_transcript_exon	Exon 1 of 2
	EMID1	ENST00000334018.11	TSL:1 MANE Select	c.823+350C>T		intron	N/A	ENSP00000335481.6
	EMID1	ENST00000404820.7	TSL:5	c.823+350C>T		intron	N/A	ENSP00000384452.3

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

African (AFR) AF: 0.0913 AC: 188 AN: 2060

American (AMR) AF: 0.366 AC: 1486 AN: 4062

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1219 AN: 2412

East Asian (EAS) AF: 0.0435 AC: 174 AN: 4000

South Asian (SAS) AF: 0.180 AC: 745 AN: 4140

European-Finnish (FIN) AF: 0.302 AC: 1166 AN: 3860

Middle Eastern (MID) AF: 0.509 AC: 167 AN: 328

European-Non Finnish (NFE) AF: 0.413 AC: 18664 AN: 45218

Other (OTH) AF: 0.388 AC: 1739 AN: 4484

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

African (AFR) AF: 0.0868 AC: 3608 AN: 41546

American (AMR) AF: 0.391 AC: 5974 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3470

East Asian (EAS) AF: 0.0641 AC: 331 AN: 5164

South Asian (SAS) AF: 0.174 AC: 837 AN: 4822

European-Finnish (FIN) AF: 0.314 AC: 3321 AN: 10592

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28219 AN: 67940

Other (OTH) AF: 0.361 AC: 762 AN: 2108

Alfa AF: 0.389 Hom.: 26159

Bravo AF: 0.300

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.65
PhyloP100		-3.8
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: rs1997719; hg19: chr22-29628741;