chr9-107601283-C-T

Variant names:

• chr9-107601283-C-T
• rs7034018
• XR_001746877.2:n.841+7786C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_930216.2(LOC105376205):​n.926+7786C>T variant causes a intron 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_930216.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 6 publications found

Genes affected

LOC105376205 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.338 AC: 14020 AN: 41454

American (AMR) AF: 0.133 AC: 2032 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3468

East Asian (EAS) AF: 0.0275 AC: 142 AN: 5172

South Asian (SAS) AF: 0.175 AC: 847 AN: 4828

European-Finnish (FIN) AF: 0.140 AC: 1483 AN: 10574

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11159 AN: 68020

Other (OTH) AF: 0.214 AC: 452 AN: 2110

Alfa AF: 0.180 Hom.: 11634

Bravo AF: 0.214

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0050
DANN	Benign	0.80
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7034018; hg19: chr9-110363564;