ENST00000415801.1:n.857+1477T>C

Variant names:

• chr9-86990383-T-C
• rs1034012
• ENST00000415801.1:n.857+1477T>C

Variant summary

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

The ENST00000415801.1(GAS1RR):​n.857+1477T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,248 control chromosomes in the GnomAD database, including 52,385 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 0.83 (52385 hom., cov: 34)
• Consequence: GAS1RR ENST00000415801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

GAS1RR (HGNC:52261): (GAS1 adjacent regulatory RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAS1RR	NR_049794.1	n.858+1477T>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAS1RR	ENST00000415801.1	n.857+1477T>C		intron_variant	Intron 5 of 6	1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125831 AN: 152130 Hom.: 52332 Cov.: 34

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.827 AC: 125939 AN: 152248 Hom.: 52385 Cov.: 34 AF XY: 0.828 AC XY: 61643 AN XY: 74442

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.811

Alfa AF: 0.802 Hom.: 10701

Bravo AF: 0.834

Asia WGS AF: 0.925 AC: 3219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1034012; hg19: chr9-89605298;