9-118150826-T-C

Position:

• chr9-118150826-T-C

Variant summary

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

The ENST00000703416.1(ENSG00000284977):​n.963T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,022 control chromosomes in the GnomAD database, including 52,779 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 0.82 (52779 hom., cov: 33)
• Consequence: ENSG00000284977 ENST00000703416.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

ENSG00000284977 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376247	XR_930293.3	n.224-15951T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284977	ENST00000703416.1	n.963T>C		non_coding_transcript_exon_variant	8/8
ENSG00000284977	ENST00000697639.1	n.1419+6464T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125221 AN: 151904 Hom.: 52759 Cov.: 33

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.824 AC: 125294 AN: 152022 Hom.: 52779 Cov.: 33 AF XY: 0.823 AC XY: 61144 AN XY: 74302

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.840

Alfa AF: 0.898 Hom.: 128129

Bravo AF: 0.800

Asia WGS AF: 0.792 AC: 2753 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2806117; hg19: chr9-120913104;