3-49033066-C-T

Variant names:

• chr3-49033066-C-T
• rs4974081
• NM_198880.3:c.1895+54G>A

Variant summary

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

The NM_198880.3(QRICH1):​c.1895+54G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 1,312,620 control chromosomes in the GnomAD database, including 414,433 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 0.82 (51327 hom., cov: 32)
  • Exomes 𝑓: 0.79 (363106 hom.)
• Consequence: QRICH1 NM_198880.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

Genes affected

QRICH1 (HGNC:24713): (glutamine rich 1) Enables DNA binding activity. Involved in several processes, including PERK-mediated unfolded protein response; intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress; and positive regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000290315 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
QRICH1	NM_198880.3	c.1895+54G>A		intron_variant	Intron 7 of 9	ENST00000395443.7	NP_942581.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
QRICH1	ENST00000395443.7	c.1895+54G>A		intron_variant	Intron 7 of 9	1	NM_198880.3	ENSP00000378830.2
ENSG00000290315	ENST00000703936.1	c.1895+54G>A		intron_variant	Intron 7 of 21			ENSP00000515567.1

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124441 AN: 152064 Hom.: 51280 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.803

GnomAD4 exome AF: 0.788 AC: 914826 AN: 1160438 Hom.: 363106 Cov.: 15 AF XY: 0.791 AC XY: 452108 AN XY: 571302

Gnomad4 AFR exome AF: 0.887

Gnomad4 AMR exome AF: 0.890

Gnomad4 ASJ exome AF: 0.870

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.936

Gnomad4 FIN exome AF: 0.793

Gnomad4 NFE exome AF: 0.763

Gnomad4 OTH exome AF: 0.809

GnomAD4 genome AF: 0.818 AC: 124548 AN: 152182 Hom.: 51327 Cov.: 32 AF XY: 0.825 AC XY: 61361 AN XY: 74396

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.806

Alfa AF: 0.791 Hom.: 13203

Bravo AF: 0.824

Asia WGS AF: 0.965 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
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: rs4974081; hg19: chr3-49070499;