22-26645319-C-G

Variant names:

• chr22-26645319-C-G
• rs16982515
• ENST00000425548.1:n.18G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ENSG00000309298 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425548.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ISCA2P1	ENST00000425548.1	TSL:6	n.18G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000309298	ENST00000840167.1		n.790+1729G>C		intron	N/A
	ENSG00000309298	ENST00000840168.1		n.214+954G>C		intron	N/A

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

African (AFR) AF: 0.142 AC: 1317 AN: 9274

American (AMR) AF: 0.0702 AC: 987 AN: 14050

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 1164 AN: 9432

East Asian (EAS) AF: 0.0544 AC: 1022 AN: 18784

South Asian (SAS) AF: 0.105 AC: 4408 AN: 42080

European-Finnish (FIN) AF: 0.133 AC: 2389 AN: 17952

Middle Eastern (MID) AF: 0.124 AC: 171 AN: 1376

European-Non Finnish (NFE) AF: 0.0802 AC: 15216 AN: 189826

Other (OTH) AF: 0.0964 AC: 1741 AN: 18068

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

African (AFR) AF: 0.136 AC: 5660 AN: 41500

American (AMR) AF: 0.0816 AC: 1247 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3470

East Asian (EAS) AF: 0.0642 AC: 332 AN: 5172

South Asian (SAS) AF: 0.115 AC: 553 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1504 AN: 10590

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0813 AC: 5530 AN: 67988

Other (OTH) AF: 0.101 AC: 214 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.42
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs16982515; hg19: chr22-27041283;