rs1277435377

Variant names:

• chr2-206162602-G-A
• rs1277435377
• NM_001959.4:c.511G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-206162602-G-A
• chr2-206162602-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001959.4(EEF1B2):​c.511G>A​(p.Val171Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000411 in 1,459,498 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V171L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000041 (0 hom.)
• Consequence: EEF1B2 NM_001959.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.34

Genes affected

EEF1B2 (HGNC:3208): (eukaryotic translation elongation factor 1 beta 2) This gene encodes a translation elongation factor. The protein is a guanine nucleotide exchange factor involved in the transfer of aminoacylated tRNAs to the ribosome. Alternative splicing results in three transcript variants which differ only in the 5' UTR. [provided by RefSeq, Jul 2008]

SNORA41 (HGNC:32634): (small nucleolar RNA, H/ACA box 41)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEF1B2	NM_001959.4	c.511G>A	p.Val171Ile	missense_variant	Exon 5 of 6	ENST00000392222.7	NP_001950.1
EEF1B2	NM_001037663.2	c.511G>A	p.Val171Ile	missense_variant	Exon 6 of 7		NP_001032752.1
EEF1B2	NM_021121.4	c.511G>A	p.Val171Ile	missense_variant	Exon 6 of 7		NP_066944.1
SNORA41	NR_002590.1	n.*243G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEF1B2	ENST00000392222.7	c.511G>A	p.Val171Ile	missense_variant	Exon 5 of 6	1	NM_001959.4	ENSP00000376056.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000411 AC: 6 AN: 1459498 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 725956

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000540

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Uncertain	0.028	T
BayesDel_noAF	Benign	-0.20
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.13	T;T;T
Eigen	Benign	0.074
Eigen_PC	Benign	0.16
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Benign	0.0059	T
MetaRNN	Uncertain	0.48	T;T;T
MetaSVM	Benign	-0.48	T
MutationAssessor	Benign	1.9	L;L;L
PrimateAI	Uncertain	0.72	T
PROVEAN	Benign	-0.13	N;N;N
REVEL	Benign	0.15
Sift	Benign	0.046	D;D;D
Sift4G	Uncertain	0.058	T;T;T
Polyphen		0.011	B;B;B
Vest4		0.53
MutPred		0.38		Gain of catalytic residue at V171 (P = 0.0761);Gain of catalytic residue at V171 (P = 0.0761);Gain of catalytic residue at V171 (P = 0.0761);
MVP		0.56
MPC		0.28
ClinPred		0.85	D
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.089
gMVP		0.18

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

Publications

LitVar

Other links and lift over

dbSNP: rs1277435377; hg19: chr2-207027326;