rs1062344

Positions:

• chr2-206003998-C-T

Variant summary

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

The NM_017759.5(INO80D):​c.*370G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 236,584 control chromosomes in the GnomAD database, including 11,136 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 0.28 (6802 hom., cov: 32)
  • Exomes 𝑓: 0.30 (4334 hom.)
• Consequence: INO80D NM_017759.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

Genes affected

INO80D (HGNC:25997): (INO80 complex subunit D) Predicted to be involved in DNA recombination and DNA repair. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INO80D	NM_017759.5	c.*370G>A		3_prime_UTR_variant	11/11	ENST00000403263.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INO80D	ENST00000403263.6	c.*370G>A		3_prime_UTR_variant	11/11	5	NM_017759.5	P1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42131 AN: 152004 Hom.: 6796 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.289

GnomAD4 exome AF: 0.302 AC: 25496 AN: 84462 Hom.: 4334 Cov.: 0 AF XY: 0.298 AC XY: 12908 AN XY: 43382

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.326

Gnomad4 ASJ exome AF: 0.356

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.330

Gnomad4 NFE exome AF: 0.350

Gnomad4 OTH exome AF: 0.315

GnomAD4 genome AF: 0.277 AC: 42154 AN: 152122 Hom.: 6802 Cov.: 32 AF XY: 0.276 AC XY: 20528 AN XY: 74368

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.286

Alfa AF: 0.324 Hom.: 3479

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	9.8
DANN	Benign	0.71

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: rs1062344; hg19: chr2-206868722;