chr9-117796733-T-C

Position:

• chr9-117796733-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000697639.1(ENSG00000284977):​n.962+9908T>C 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 0.678 in 151,856 control chromosomes in the GnomAD database, including 35,431 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 0.68 (35431 hom., cov: 33)
• Consequence: ENST00000697639.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376244	XR_007061905.1	n.2829-6248T>C		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061906.1	n.2246-6248T>C		intron_variant, non_coding_transcript_variant
LOC105376244	XR_007061907.1	n.2146+29483T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000697639.1	n.962+9908T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102905 AN: 151738 Hom.: 35403 Cov.: 33

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.678 AC: 102983 AN: 151856 Hom.: 35431 Cov.: 33 AF XY: 0.688 AC XY: 51036 AN XY: 74188

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.675

Alfa AF: 0.629 Hom.: 4865

Bravo AF: 0.673

Asia WGS AF: 0.846 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	17
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10115586; hg19: chr9-120559011;