3-40284674-C-T

Variant names:

• chr3-40284674-C-T
• rs11129874
• ENST00000625390.2:n.380+16563G>A

Variant summary

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

The ENST00000625390.2(EIF1B-AS1):​n.380+16563G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,878 control chromosomes in the GnomAD database, including 16,053 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 0.42 (16053 hom., cov: 33)
• Consequence: EIF1B-AS1 ENST00000625390.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 8 publications found

Genes affected

EIF1B-AS1 (HGNC:):

EIF1B-AS1 (HGNC:44555): (EIF1B antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF1B-AS1	NR_033965.1	n.536+16563G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF1B-AS1	ENST00000625390.2	n.380+16563G>A		intron_variant	Intron 2 of 2	1
EIF1B-AS1	ENST00000631175.3	n.536+16563G>A		intron_variant	Intron 2 of 4	1
EIF1B-AS1	ENST00000626073.2	n.831+16563G>A		intron_variant	Intron 2 of 4	6

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63390 AN: 151760 Hom.: 16049 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.417

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.417 AC: 63397 AN: 151878 Hom.: 16053 Cov.: 33 AF XY: 0.418 AC XY: 31072 AN XY: 74252

African (AFR) AF: 0.125 AC: 5179 AN: 41422

American (AMR) AF: 0.491 AC: 7486 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1337 AN: 5176

South Asian (SAS) AF: 0.365 AC: 1761 AN: 4824

European-Finnish (FIN) AF: 0.591 AC: 6197 AN: 10478

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38564 AN: 67938

Other (OTH) AF: 0.415 AC: 876 AN: 2110

Alfa AF: 0.505 Hom.: 13794

Bravo AF: 0.396

Asia WGS AF: 0.296 AC: 1023 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.8
DANN	Benign	0.92
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs11129874; hg19: chr3-40326165;