chr1-121538815-A-G

Position:

• chr1-121538815-A-G

Variant summary

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

The NR_003955.1(EMBP1):​n.349-17695A>G variant causes a intron, non coding transcript 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 NR_003955.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMBP1	NR_003955.1	n.349-17695A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMBP1	ENST00000458200.2	n.116-17695A>G		intron_variant, non_coding_transcript_variant
EMBP1	ENST00000648011.3	n.435+395A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.334

Alfa AF: 0.381 Hom.: 23271

Bravo AF: 0.279

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11249433; hg19: chr1-121280613;