5-50397624-C-T

Variant names:

• chr5-50397624-C-T
• rs2883164
• NM_198449.3:c.*1649G>A

Variant summary

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

The NM_198449.3(EMB):​c.*1649G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,896 control chromosomes in the GnomAD database, including 20,511 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 0.51 (20511 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: EMB NM_198449.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 3 publications found

Genes affected

EMB (HGNC:30465): (embigin) This gene encodes a transmembrane glycoprotein that is a member of the immunoglobulin superfamily. The encoded protein may be involved in cell growth and development by mediating interactions between the cell and extracellular matrix. A pseudogene of this gene is found on chromosome 1. [provided by RefSeq, Jan 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMB	NM_198449.3	c.*1649G>A		3_prime_UTR_variant	Exon 9 of 9	ENST00000303221.10	NP_940851.1
EMB	XM_011543146.3	c.*1649G>A		3_prime_UTR_variant	Exon 10 of 10		XP_011541448.1
EMB	XM_047416702.1	c.*1649G>A		3_prime_UTR_variant	Exon 9 of 9		XP_047272658.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMB	ENST00000303221.10	c.*1649G>A		3_prime_UTR_variant	Exon 9 of 9	1	NM_198449.3	ENSP00000302289.5

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77012 AN: 151778 Hom.: 20486 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.477

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.508 AC: 77093 AN: 151896 Hom.: 20511 Cov.: 32 AF XY: 0.501 AC XY: 37225 AN XY: 74248

African (AFR) AF: 0.669 AC: 27713 AN: 41444

American (AMR) AF: 0.454 AC: 6924 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1956 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2550 AN: 5162

South Asian (SAS) AF: 0.503 AC: 2421 AN: 4816

European-Finnish (FIN) AF: 0.340 AC: 3582 AN: 10538

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30471 AN: 67912

Other (OTH) AF: 0.477 AC: 1008 AN: 2114

Alfa AF: 0.474 Hom.: 2342

Bravo AF: 0.521

Asia WGS AF: 0.503 AC: 1742 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		-0.057
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: rs2883164; hg19: chr5-49693458;