1-121559216-G-C

Variant names:

• chr1-121559216-G-C
• rs6600745
• ENST00000458200.2:n.391+2197G>C

Variant summary

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

The ENST00000622787.5(EMBP1):​n.698+2197G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,678 control chromosomes in the GnomAD database, including 24,296 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 0.56 (24296 hom., cov: 32)
• Consequence: EMBP1 ENST00000622787.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.84
• Publications: 7 publications found

Genes affected

EMBP1 (HGNC:38661): (embigin pseudogene 1)

EMBP1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000622787.5. 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
	EMBP1	NR_003955.1		n.624+2197G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMBP1	ENST00000458200.2	TSL:6	n.391+2197G>C		intron	N/A
	EMBP1	ENST00000618253.2	TSL:4	n.731+2197G>C		intron	N/A
	EMBP1	ENST00000622787.5	TSL:2	n.698+2197G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85573 AN: 151562 Hom.: 24271 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.581

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.565 AC: 85651 AN: 151678 Hom.: 24296 Cov.: 32 AF XY: 0.564 AC XY: 41807 AN XY: 74086

African (AFR) AF: 0.502 AC: 20745 AN: 41354

American (AMR) AF: 0.578 AC: 8767 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2597 AN: 5156

South Asian (SAS) AF: 0.400 AC: 1924 AN: 4812

European-Finnish (FIN) AF: 0.646 AC: 6813 AN: 10552

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41108 AN: 67864

Other (OTH) AF: 0.577 AC: 1215 AN: 2106

Alfa AF: 0.465 Hom.: 1282

Bravo AF: 0.565

Asia WGS AF: 0.443 AC: 1544 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	0.011
DANN	Benign	0.69
PhyloP100		-4.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6600745;

hg19: chr1-121301014;