rs2270797

Positions:

• chr12-148821-C-T

Variant summary

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

The NM_001170738.2(IQSEC3):​c.2153+7536C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 152,112 control chromosomes in the GnomAD database, including 817 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 0.084 (817 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IQSEC3 NM_001170738.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

IQSEC3 (HGNC:29193): (IQ motif and Sec7 domain ArfGEF 3) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including actin cytoskeleton organization; activation of GTPase activity; and regulation of small GTPase mediated signal transduction. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IQSEC3	NM_001170738.2	c.2153+7536C>T		intron_variant		ENST00000538872.6
LOC574538	NR_033859.2	n.91+258G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQSEC3	ENST00000538872.6	c.2153+7536C>T		intron_variant		5	NM_001170738.2	P1
	ENST00000508953.2	n.295G>A		non_coding_transcript_exon_variant	1/7	1
	ENST00000505893.6	n.91+258G>A		intron_variant, non_coding_transcript_variant		2
IQSEC3	ENST00000382841.2	c.1244+7536C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12759 AN: 151994 Hom.: 817 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0426

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0861

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0840 AC: 12772 AN: 152112 Hom.: 817 Cov.: 32 AF XY: 0.0886 AC XY: 6592 AN XY: 74378

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0484

Gnomad4 ASJ AF: 0.0426

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.0761

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.0523 Hom.: 602

Bravo AF: 0.0824

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.63

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: rs2270797; hg19: chr12-257987;