chr9-107633792-C-T

Position:

• chr9-107633792-C-T

Variant summary

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

The XR_930217.2(LOC105376205):​n.1287+2113C>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 152,158 control chromosomes in the GnomAD database, including 1,321 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 (1321 hom., cov: 33)
• Consequence: LOC105376205 XR_930217.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

Genes affected

LOC105376205 (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 (NFE) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376205	XR_930217.2	n.1287+2113C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17684 AN: 152040 Hom.: 1321 Cov.: 33

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.116 AC: 17695 AN: 152158 Hom.: 1321 Cov.: 33 AF XY: 0.115 AC XY: 8526 AN XY: 74378

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.0943

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.127

Alfa AF: 0.156 Hom.: 2588

Bravo AF: 0.106

Asia WGS AF: 0.0650 AC: 224 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	2.8
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: rs11794132; hg19: chr9-110396073; COSMIC: COSV62691003;