2-74458316-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_037849.1(INO80B-WBP1):n.1161+456T>G 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 0.136 in 673,140 control chromosomes in the GnomAD database, including 7,759 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 0.11 (1371 hom., cov: 33)
  • Exomes 𝑓: 0.14 (6388 hom.)
• Consequence: INO80B-WBP1 NR_037849.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18

Genes affected

INO80B-WBP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INO80B-WBP1	NR_037849.1	n.1161+456T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16955 AN: 152118 Hom.: 1372 Cov.: 33

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.107

GnomAD4 exome AF: 0.143 AC: 74469 AN: 520904 Hom.: 6388 Cov.: 7 AF XY: 0.140 AC XY: 37214 AN XY: 266250

Gnomad4 AFR exome AF: 0.0276

Gnomad4 AMR exome AF: 0.0660

Gnomad4 ASJ exome AF: 0.113

Gnomad4 EAS exome AF: 0.0000712

Gnomad4 SAS exome AF: 0.0361

Gnomad4 FIN exome AF: 0.244

Gnomad4 NFE exome AF: 0.166

Gnomad4 OTH exome AF: 0.129

GnomAD4 genome AF: 0.111 AC: 16947 AN: 152236 Hom.: 1371 Cov.: 33 AF XY: 0.111 AC XY: 8288 AN XY: 74424

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.0693

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0376

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.106

Alfa AF: 0.139 Hom.: 1693

Bravo AF: 0.0941

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
Cadd	Benign	18
Dann	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs34174194; hg19: chr2-74685443;