9-1786681-T-G

Variant names:

• chr9-1786681-T-G
• rs7048135
• XR_001746599.1:n.142+67769T>G

Variant summary

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

The XR_001746599.1(LOC105375951):​n.142+67769T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,056 control chromosomes in the GnomAD database, including 4,860 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 0.24 (4860 hom., cov: 32)
• Consequence: LOC105375951 XR_001746599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 1 publications found

Genes affected

LOC105375951 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35827 AN: 151938 Hom.: 4839 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.236 AC: 35900 AN: 152056 Hom.: 4860 Cov.: 32 AF XY: 0.239 AC XY: 17732 AN XY: 74338

African (AFR) AF: 0.364 AC: 15085 AN: 41454

American (AMR) AF: 0.219 AC: 3352 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1891 AN: 5126

South Asian (SAS) AF: 0.160 AC: 771 AN: 4812

European-Finnish (FIN) AF: 0.226 AC: 2392 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11064 AN: 68002

Other (OTH) AF: 0.258 AC: 545 AN: 2112

Alfa AF: 0.191 Hom.: 8525

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0050
DANN	Benign	0.32
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7048135; hg19: chr9-1786681;