1-121538815-A-G

Variant names:

• chr1-121538815-A-G
• rs11249433
• ENST00000458200.2:n.116-17695A>G

Variant summary

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

The ENST00000622787.5(EMBP1):​n.423-17695A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,082 control chromosomes in the GnomAD database, including 7,883 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 0.29 (7883 hom., cov: 32)
• Consequence: EMBP1 ENST00000622787.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 192 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 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.349-17695A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMBP1	ENST00000458200.2	TSL:6	n.116-17695A>G		intron	N/A
	EMBP1	ENST00000618253.2	TSL:4	n.455+395A>G		intron	N/A
	EMBP1	ENST00000622787.5	TSL:2	n.423-17695A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43949 AN: 151964 Hom.: 7879 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.289 AC: 43959 AN: 152082 Hom.: 7883 Cov.: 32 AF XY: 0.284 AC XY: 21084 AN XY: 74340

African (AFR) AF: 0.113 AC: 4706 AN: 41502

American (AMR) AF: 0.281 AC: 4299 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1541 AN: 3472

East Asian (EAS) AF: 0.0299 AC: 155 AN: 5186

South Asian (SAS) AF: 0.202 AC: 972 AN: 4814

European-Finnish (FIN) AF: 0.335 AC: 3535 AN: 10564

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27621 AN: 67944

Other (OTH) AF: 0.334 AC: 707 AN: 2116

Alfa AF: 0.368 Hom.: 47972

Bravo AF: 0.279

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.73
PhyloP100		-0.44

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: rs11249433;

hg19: chr1-121280613;