9-84564647-A-G

Position:

• chr9-84564647-A-G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-18550A>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 0.0982 in 152,128 control chromosomes in the GnomAD database, including 883 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 0.098 (883 hom., cov: 32)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724036	XR_007061623.1	n.6209+6593A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650453.1	n.979-18550A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14898 AN: 152010 Hom.: 876 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0872

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0895

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

GnomAD4 genome AF: 0.0982 AC: 14937 AN: 152128 Hom.: 883 Cov.: 32 AF XY: 0.0988 AC XY: 7345 AN XY: 74370

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.0567

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.0872

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0729 Hom.: 243

Bravo AF: 0.107

Asia WGS AF: 0.0670 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512149; hg19: chr9-87179562;