9-115662708-A-T

Position:

• chr9-115662708-A-T

Variant summary

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

The ENST00000646338.1(ENSG00000228714):​n.275+78754T>A 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 0.117 in 151,708 control chromosomes in the GnomAD database, including 1,124 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 (1124 hom., cov: 32)
• Consequence: ENST00000646338.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376235	XR_930270.3	n.145-1676A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646338.1	n.275+78754T>A		intron_variant, non_coding_transcript_variant
	ENST00000644998.1	n.196-20727T>A		intron_variant, non_coding_transcript_variant
	ENST00000645745.1	n.422+26516T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17812 AN: 151590 Hom.: 1127 Cov.: 32

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.117 AC: 17814 AN: 151708 Hom.: 1124 Cov.: 32 AF XY: 0.116 AC XY: 8637 AN XY: 74156

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.111

Alfa AF: 0.128 Hom.: 166

Bravo AF: 0.113

Asia WGS AF: 0.111 AC: 388 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12006166; hg19: chr9-118424987;