rs13433297

chr20-13319088-G-A

Variant summary

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

The XM_017027680.2(ISM1):c.878-5978G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,150 control chromosomes in the GnomAD database, including 1,528 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 0.12 (1528 hom., cov: 32)
• Consequence: ISM1 XM_017027680.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

ISM1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ISM1	XM_017027680.2	c.878-5978G>A		intron_variant
TASP1	XM_047440269.1	c.1171-3033C>T		intron_variant
TASP1	XR_001754319.3	n.1284-3033C>T		intron_variant, non_coding_transcript_variant
TASP1	XR_007067463.1	n.1284-3033C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18105 AN: 152032 Hom.: 1528 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0879

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.108

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.119 AC: 18109 AN: 152150 Hom.: 1528 Cov.: 32 AF XY: 0.117 AC XY: 8694 AN XY: 74392

Gnomad4 AFR AF: 0.0315

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.0625

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.107

Alfa AF: 0.159 Hom.: 975

Bravo AF: 0.107

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.8
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13433297; hg19: chr20-13299735;