3-184134987-C-A

Position:

• chr3-184134987-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_183718.1(EIF2B5-DT):​n.67+208G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 273,858 control chromosomes in the GnomAD database, including 1,802 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.095 (939 hom., cov: 33)
  • Exomes 𝑓: 0.11 (863 hom.)
• Consequence: EIF2B5-DT NR_183718.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.609

Genes affected

EIF2B5-DT (HGNC:55202): (EIF2B5 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 3-184134987-C-A is Benign according to our data. Variant chr3-184134987-C-A is described in ClinVar as [Benign]. Clinvar id is 1177820.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EIF2B5-DT	NR_183718.1	n.67+208G>T		intron_variant, non_coding_transcript_variant
EIF2B5-DT	NR_183721.1	n.275G>T		non_coding_transcript_exon_variant	1/2
EIF2B5-DT	NR_183719.1	n.67+208G>T		intron_variant, non_coding_transcript_variant
EIF2B5-DT	NR_183720.1	n.104+171G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EIF2B5-DT	ENST00000608135.1	n.44+208G>T		intron_variant, non_coding_transcript_variant		5
EIF2B5-DT	ENST00000608232.5	n.24+171G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14485 AN: 152118 Hom.: 939 Cov.: 33

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.0962

GnomAD4 exome AF: 0.107 AC: 13073 AN: 121622 Hom.: 863 AF XY: 0.106 AC XY: 6795 AN XY: 64028

Gnomad4 AFR exome AF: 0.0187

Gnomad4 AMR exome AF: 0.0629

Gnomad4 ASJ exome AF: 0.103

Gnomad4 EAS exome AF: 0.000671

Gnomad4 SAS exome AF: 0.0976

Gnomad4 FIN exome AF: 0.0859

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.0951 AC: 14483 AN: 152236 Hom.: 939 Cov.: 33 AF XY: 0.0908 AC XY: 6756 AN XY: 74440

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.0907

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.0925 Hom.: 223

Bravo AF: 0.0907

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.1
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs73185704; hg19: chr3-183852775;