rs16982515

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr22-26645319-C-A
• chr22-26645319-C-G
• chr22-26645319-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000425548.1(ISCA2P1):​n.18G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ISCA2P1 ENST00000425548.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 0 publications found

Genes affected

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

ENSG00000309298 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ISCA2P1		n.26645319C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ISCA2P1	ENST00000425548.1	n.18G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000309298	ENST00000840167.1	n.790+1729G>T		intron_variant	Intron 1 of 1
ENSG00000309298	ENST00000840168.1	n.214+954G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 321216 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 171354

African (AFR) AF: 0.00 AC: 0 AN: 9282

American (AMR) AF: 0.00 AC: 0 AN: 14058

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9442

East Asian (EAS) AF: 0.00 AC: 0 AN: 18794

South Asian (SAS) AF: 0.00 AC: 0 AN: 42106

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17996

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1378

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 190064

Other (OTH) AF: 0.00 AC: 0 AN: 18096

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.53
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;