rs274946

Positions:

• chr9-23585352-T-C

Variant summary

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

The NR_121602.1(LOC101929563):​n.1846+17333A>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 0.455 in 152,084 control chromosomes in the GnomAD database, including 16,155 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 0.46 (16155 hom., cov: 33)
• Consequence: LOC101929563 NR_121602.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929563	NR_121602.1	n.1846+17333A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000640307.1	n.1834+17333A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69235 AN: 151964 Hom.: 16146 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.455 AC: 69257 AN: 152084 Hom.: 16155 Cov.: 33 AF XY: 0.453 AC XY: 33642 AN XY: 74330

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.479

Alfa AF: 0.485 Hom.: 35558

Bravo AF: 0.447

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs274946; hg19: chr9-23585350;