chr9-3792613-C-G

Variant names:

• chr9-3792613-C-G
• rs1455177
• XR_929442.3:n.481+256C>G

Variant summary

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

The XR_929442.3(LOC105375962):​n.481+256C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,876 control chromosomes in the GnomAD database, including 16,356 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 0.45 (16356 hom., cov: 31)
• Consequence: LOC105375962 XR_929442.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 2 publications found

Genes affected

LOC105375962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 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: 0.447 AC: 67833 AN: 151756 Hom.: 16355 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.447 AC: 67844 AN: 151876 Hom.: 16356 Cov.: 31 AF XY: 0.439 AC XY: 32607 AN XY: 74220

African (AFR) AF: 0.275 AC: 11363 AN: 41378

American (AMR) AF: 0.436 AC: 6652 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2716 AN: 5180

South Asian (SAS) AF: 0.442 AC: 2127 AN: 4808

European-Finnish (FIN) AF: 0.391 AC: 4118 AN: 10528

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37159 AN: 67934

Other (OTH) AF: 0.491 AC: 1036 AN: 2108

Alfa AF: 0.488 Hom.: 2319

Bravo AF: 0.442

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.082
DANN	Benign	0.43
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1455177; hg19: chr9-3792613;