2-57048839-A-G

Variant names:

• chr2-57048839-A-G
• rs9309291
• ENST00000604970.1:n.498T>C

Variant summary

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

The ENST00000604970.1(EIF2S2P7):​n.498T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 176,308 control chromosomes in the GnomAD database, including 60,525 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 0.82 (51830 hom., cov: 32)
  • Exomes 𝑓: 0.85 (8695 hom.)
• Consequence: EIF2S2P7 ENST00000604970.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 3 publications found

Genes affected

EIF2S2P7 (HGNC:37795): (eukaryotic translation initiation factor 2 subunit 2 beta pseudogene 7)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000604970.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF2S2P7	ENST00000604970.1	TSL:6	n.498T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124684 AN: 152034 Hom.: 51767 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.813

GnomAD4 exome AF: 0.850 AC: 20522 AN: 24156 Hom.: 8695 Cov.: 0 AF XY: 0.853 AC XY: 12300 AN XY: 14414

African (AFR) AF: 0.965 AC: 714 AN: 740

American (AMR) AF: 0.810 AC: 2228 AN: 2750

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 320 AN: 402

East Asian (EAS) AF: 0.888 AC: 1433 AN: 1614

South Asian (SAS) AF: 0.883 AC: 2178 AN: 2466

European-Finnish (FIN) AF: 0.825 AC: 3727 AN: 4520

Middle Eastern (MID) AF: 0.893 AC: 25 AN: 28

European-Non Finnish (NFE) AF: 0.851 AC: 9176 AN: 10784

Other (OTH) AF: 0.846 AC: 721 AN: 852

GnomAD4 genome AF: 0.820 AC: 124811 AN: 152152 Hom.: 51830 Cov.: 32 AF XY: 0.818 AC XY: 60851 AN XY: 74378

African (AFR) AF: 0.949 AC: 39422 AN: 41544

American (AMR) AF: 0.720 AC: 10978 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2612 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4371 AN: 5168

South Asian (SAS) AF: 0.812 AC: 3915 AN: 4822

European-Finnish (FIN) AF: 0.773 AC: 8187 AN: 10594

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52527 AN: 67978

Other (OTH) AF: 0.813 AC: 1718 AN: 2114

Alfa AF: 0.756 Hom.: 4473

Bravo AF: 0.823

Asia WGS AF: 0.843 AC: 2931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.4
DANN	Benign	0.75
PhyloP100		1.7

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: rs9309291;

hg19: chr2-57275974;