15-67517652-G-A

Position:

• chr15-67517652-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000561232.5(IQCH-AS1):​n.429+1348C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00542 in 152,278 control chromosomes in the GnomAD database, including 6 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 0.0054 (6 hom., cov: 32)
• Consequence: IQCH-AS1 ENST00000561232.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

Genes affected

IQCH-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IQCH-AS1	NR_040051.1	n.402+1348C>T		intron_variant
IQCH-AS1	NR_040052.1	n.429+1348C>T		intron_variant
IQCH-AS1	NR_040054.1	n.454+1348C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IQCH-AS1	ENST00000561232.5	n.429+1348C>T		intron_variant		1
IQCH-AS1	ENST00000559285.1	n.274+1348C>T		intron_variant		2
IQCH-AS1	ENST00000559298.5	n.91+3894C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00543 AC: 826 AN: 152160 Hom.: 6 Cov.: 32

Gnomad AFR AF: 0.00176

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.00295

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00986

Gnomad OTH AF: 0.00431

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

GnomAD4 genome AF: 0.00542 AC: 825 AN: 152278 Hom.: 6 Cov.: 32 AF XY: 0.00465 AC XY: 346 AN XY: 74442

Gnomad4 AFR AF: 0.00176

Gnomad4 AMR AF: 0.00294

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00986

Gnomad4 OTH AF: 0.00426

Alfa AF: 0.00598 Hom.: 1

Bravo AF: 0.00540

Asia WGS AF: 0.000867 AC: 3 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72747452; hg19: chr15-67809990;