9-84558182-G-T

Position:

• chr9-84558182-G-T

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-25015G>T 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 0.4 in 151,878 control chromosomes in the GnomAD database, including 15,345 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 0.40 (15345 hom., cov: 33)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724036	XR_007061623.1	n.6209+128G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650453.1	n.979-25015G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60680 AN: 151760 Hom.: 15290 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.400 AC: 60804 AN: 151878 Hom.: 15345 Cov.: 33 AF XY: 0.400 AC XY: 29727 AN XY: 74264

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.363

Alfa AF: 0.275 Hom.: 6077

Bravo AF: 0.425

Asia WGS AF: 0.470 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347857; hg19: chr9-87173097;