3-40284674-C-T

Position:

• chr3-40284674-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033965.1(EIF1B-AS1):​n.536+16563G>A 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 0.417 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 NR_033965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
EIF1B-AS1	NR_033965.1	n.536+16563G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIF1B-AS1	ENST00000657703.1	n.90+16563G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.415

Alfa AF: 0.510 Hom.: 11836

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11129874; hg19: chr3-40326165;