chr20-13294555-G-C

Position:

• chr20-13294555-G-C

Variant summary

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

The NM_080826.2(ISM1):​c.877+2092G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,184 control chromosomes in the GnomAD database, including 1,356 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 (1356 hom., cov: 32)
• Consequence: ISM1 NM_080826.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

ISM1 (HGNC:16213): (isthmin 1) Predicted to be involved in negative regulation of angiogenesis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

TASP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ISM1	NM_080826.2	c.877+2092G>C		intron_variant		ENST00000262487.5	NP_543016.1
ISM1	XM_017027680.2	c.877+2092G>C		intron_variant			XP_016883169.1
TASP1	XR_001754319.3	n.1369+21415C>G		intron_variant
TASP1	XR_007067463.1	n.1369+21415C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ISM1	ENST00000262487.5	c.877+2092G>C		intron_variant		5	NM_080826.2	ENSP00000262487.3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18002 AN: 152066 Hom.: 1355 Cov.: 32

Gnomad AFR AF: 0.0629

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.118 AC: 17990 AN: 152184 Hom.: 1356 Cov.: 32 AF XY: 0.114 AC XY: 8503 AN XY: 74394

Gnomad4 AFR AF: 0.0627

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.153

Alfa AF: 0.0512 Hom.: 54

Bravo AF: 0.119

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs6074585; hg19: chr20-13275202;