rs1397618

Variant names:

• chr10-119073163-A-C
• rs1397618
• NM_003750.4:c.378-110T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-119073163-A-C
• chr10-119073163-A-G
• chr10-119073163-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003750.4(EIF3A):​c.378-110T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: EIF3A NM_003750.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 10 publications found

Genes affected

EIF3A (HGNC:3271): (eukaryotic translation initiation factor 3 subunit A) Enables RNA binding activity. Contributes to translation initiation factor activity. Involved in IRES-dependent viral translational initiation; formation of cytoplasmic translation initiation complex; and viral translational termination-reinitiation. Located in cytosol; nucleolus; and nucleoplasm. Part of eukaryotic translation initiation factor 3 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF3A	NM_003750.4	c.378-110T>G		intron_variant	Intron 3 of 21	ENST00000369144.8	NP_003741.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF3A	ENST00000369144.8	c.378-110T>G		intron_variant	Intron 3 of 21	1	NM_003750.4	ENSP00000358140.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 905292 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 456050

African (AFR) AF: 0.00 AC: 0 AN: 20434

American (AMR) AF: 0.00 AC: 0 AN: 20978

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16936

East Asian (EAS) AF: 0.00 AC: 0 AN: 33594

South Asian (SAS) AF: 0.00 AC: 0 AN: 55910

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33826

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3060

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 679486

Other (OTH) AF: 0.00 AC: 0 AN: 41068

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.085
DANN	Benign	0.25
PhyloP100		-2.0

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: rs1397618; hg19: chr10-120832675;