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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF2S2P7		n.57048839A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF2S2P7	ENST00000604970.1	n.498T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs9309291; hg19: chr2-57275974;