rs1223271

chr20-13316265-G-Achr20-13316265-G-C

Variant summary

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

The XM_017027680.2(ISM1):c.878-8801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,810 control chromosomes in the GnomAD database, including 1,700 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 (1700 hom., cov: 32)
• Consequence: ISM1 XM_017027680.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515

Genes affected

ISM1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ISM1	XM_017027680.2	c.878-8801G>A		intron_variant
TASP1	XM_047440269.1	c.1171-210C>T		intron_variant
TASP1	XR_001754319.3	n.1284-210C>T		intron_variant, non_coding_transcript_variant
TASP1	XR_007067463.1	n.1284-210C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18485 AN: 151694 Hom.: 1698 Cov.: 32

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.122 AC: 18483 AN: 151810 Hom.: 1700 Cov.: 32 AF XY: 0.128 AC XY: 9473 AN XY: 74198

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.135

Alfa AF: 0.144 Hom.: 3962

Bravo AF: 0.118

Asia WGS AF: 0.342 AC: 1188 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1223271; hg19: chr20-13296912;