rs16982515

chr22-26645319-C-Gchr22-26645319-C-T

Variant summary

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

The ENST00000425548.1(ISCA2P1):n.18G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 472,994 control chromosomes in the GnomAD database, including 2,232 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 0.10 (883 hom., cov: 32)
  • Exomes 𝑓: 0.089 (1349 hom.)
• Consequence: ISCA2P1 ENST00000425548.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

ISCA2P1 (HGNC:38022): (iron-sulfur cluster assembly 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ISCA2P1	ENST00000425548.1	n.18G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15570 AN: 152034 Hom.: 878 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.0998

GnomAD4 exome AF: 0.0886 AC: 28415 AN: 320842 Hom.: 1349 Cov.: 0 AF XY: 0.0893 AC XY: 15290 AN XY: 171144

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.0702

Gnomad4 ASJ exome AF: 0.123

Gnomad4 EAS exome AF: 0.0544

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.0802

Gnomad4 OTH exome AF: 0.0964

GnomAD4 genome AF: 0.102 AC: 15593 AN: 152152 Hom.: 883 Cov.: 32 AF XY: 0.106 AC XY: 7853 AN XY: 74382

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.0642

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.0813

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0398 Hom.: 30

Bravo AF: 0.0980

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.9
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16982515; hg19: chr22-27041283;