9-1456797-C-T

Variant names:

• chr9-1456797-C-T
• rs1412259
• XR_002956872.2:n.357-7346C>T

Variant summary

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

The XR_929415.3(LOC102723803):​n.357-7346C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,796 control chromosomes in the GnomAD database, including 10,506 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 0.37 (10506 hom., cov: 32)
• Consequence: LOC102723803 XR_929415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 6 publications found

Genes affected

LOC102723803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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: 0.368 AC: 55779 AN: 151678 Hom.: 10510 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.367 AC: 55785 AN: 151796 Hom.: 10506 Cov.: 32 AF XY: 0.360 AC XY: 26702 AN XY: 74154

African (AFR) AF: 0.318 AC: 13149 AN: 41400

American (AMR) AF: 0.342 AC: 5214 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1444 AN: 3464

East Asian (EAS) AF: 0.179 AC: 918 AN: 5132

South Asian (SAS) AF: 0.393 AC: 1893 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3076 AN: 10520

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28773 AN: 67918

Other (OTH) AF: 0.385 AC: 814 AN: 2112

Alfa AF: 0.387 Hom.: 17326

Bravo AF: 0.367

Asia WGS AF: 0.287 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1412259; hg19: chr9-1456797;