rs1020884

chr9-97395770-T-C

Variant summary

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

The NR_026847.1(LOC286359):n.322+280A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,084 control chromosomes in the GnomAD database, including 12,321 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 0.39 (12321 hom., cov: 32)
• Consequence: LOC286359 NR_026847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC286359	NR_026847.1	n.322+280A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000430691.1	n.106+237A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58836 AN: 151966 Hom.: 12304 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.387 AC: 58880 AN: 152084 Hom.: 12321 Cov.: 32 AF XY: 0.383 AC XY: 28504 AN XY: 74370

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.415

Alfa AF: 0.450 Hom.: 22454

Bravo AF: 0.390

Asia WGS AF: 0.412 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.4
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1020884; hg19: chr9-100158052;