1-121563523-C-T

Variant names:

• chr1-121563523-C-T
• rs4259688
• ENST00000458200.2:n.520-1114C>T

Variant summary

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

The ENST00000622787.5(EMBP1):​n.827-1114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,722 control chromosomes in the GnomAD database, including 19,859 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 0.49 (19859 hom., cov: 32)
• Consequence: EMBP1 ENST00000622787.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 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.753-1114C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMBP1	ENST00000458200.2	TSL:6	n.520-1114C>T		intron	N/A
	EMBP1	ENST00000618253.2	TSL:4	n.860-1114C>T		intron	N/A
	EMBP1	ENST00000622787.5	TSL:2	n.827-1114C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74571 AN: 151604 Hom.: 19855 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.492 AC: 74591 AN: 151722 Hom.: 19859 Cov.: 32 AF XY: 0.491 AC XY: 36424 AN XY: 74144

African (AFR) AF: 0.268 AC: 11119 AN: 41426

American (AMR) AF: 0.529 AC: 8031 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1825 AN: 3460

East Asian (EAS) AF: 0.535 AC: 2750 AN: 5136

South Asian (SAS) AF: 0.391 AC: 1884 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6414 AN: 10546

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.603 AC: 40879 AN: 67832

Other (OTH) AF: 0.519 AC: 1092 AN: 2106

Alfa AF: 0.569 Hom.: 18280

Bravo AF: 0.483

Asia WGS AF: 0.430 AC: 1499 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	4.5
DANN	Benign	0.38
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs4259688; hg19: chr1-121305321;