rs1062344

Variant names:

• chr2-206003998-C-T
• rs1062344
• NM_017759.5:c.*370G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
INO80D	NM_017759.5	c.*370G>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000403263.6	NP_060229.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INO80D	ENST00000403263.6	c.*370G>A		3_prime_UTR_variant	Exon 11 of 11	5	NM_017759.5	ENSP00000384198.1

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

African (AFR) AF: 0.114 AC: 485 AN: 4254

American (AMR) AF: 0.326 AC: 1500 AN: 4604

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 847 AN: 2376

East Asian (EAS) AF: 0.148 AC: 896 AN: 6072

South Asian (SAS) AF: 0.159 AC: 1230 AN: 7748

European-Finnish (FIN) AF: 0.330 AC: 1106 AN: 3350

Middle Eastern (MID) AF: 0.282 AC: 98 AN: 348

European-Non Finnish (NFE) AF: 0.350 AC: 17878 AN: 51084

Other (OTH) AF: 0.315 AC: 1456 AN: 4626

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

African (AFR) AF: 0.121 AC: 5033 AN: 41530

American (AMR) AF: 0.354 AC: 5402 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3466

East Asian (EAS) AF: 0.144 AC: 745 AN: 5178

South Asian (SAS) AF: 0.154 AC: 739 AN: 4814

European-Finnish (FIN) AF: 0.358 AC: 3785 AN: 10580

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24197 AN: 67974

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.325 Hom.: 4131

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
PhyloP100		-0.044
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1062344; hg19: chr2-206868722;