9-84650211-C-T

Position:

• chr9-84650211-C-T

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.1342-5003C>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 0.116 in 142,666 control chromosomes in the GnomAD database, including 1,162 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 0.12 (1162 hom., cov: 28)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724036	XR_007061623.1	n.7631-3208C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650453.1	n.1342-5003C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 16555 AN: 142590 Hom.: 1155 Cov.: 28

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.116 AC: 16578 AN: 142666 Hom.: 1162 Cov.: 28 AF XY: 0.120 AC XY: 8229 AN XY: 68646

Gnomad4 AFR AF: 0.0605

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0599

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.161

Alfa AF: 0.102 Hom.: 119

Bravo AF: 0.118

Asia WGS AF: 0.270 AC: 937 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10868223; hg19: chr9-87265126;