9-107601283-C-T

Position:

• chr9-107601283-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.926+7786C>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 0.207 in 152,114 control chromosomes in the GnomAD database, including 3,895 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 0.21 (3895 hom., cov: 32)
• Consequence: LOC105376205 XR_930217.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

LOC105376205 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376205	XR_930217.2	n.926+7786C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31437 AN: 151996 Hom.: 3889 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.207 AC: 31456 AN: 152114 Hom.: 3895 Cov.: 32 AF XY: 0.203 AC XY: 15067 AN XY: 74356

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0275

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.214

Alfa AF: 0.174 Hom.: 5250

Bravo AF: 0.214

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7034018; hg19: chr9-110363564;