rs1412256

Variant names:

• chr9-1464067-C-G
• rs1412256
• XR_002956872.2:n.357-76C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-1464067-C-G
• chr9-1464067-C-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.357-76C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,980 control chromosomes in the GnomAD database, including 2,875 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 0.14 (2875 hom., cov: 32)
• Consequence: LOC102723803 XR_929415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.142 AC: 21629 AN: 151862 Hom.: 2865 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0798

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.143 AC: 21674 AN: 151980 Hom.: 2875 Cov.: 32 AF XY: 0.137 AC XY: 10197 AN XY: 74262

African (AFR) AF: 0.354 AC: 14667 AN: 41402

American (AMR) AF: 0.0694 AC: 1059 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.0798 AC: 411 AN: 5150

South Asian (SAS) AF: 0.0868 AC: 418 AN: 4816

European-Finnish (FIN) AF: 0.0248 AC: 263 AN: 10584

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4041 AN: 67988

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.0390 Hom.: 53

Bravo AF: 0.155

Asia WGS AF: 0.0870 AC: 305 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	1.2
DANN	Benign	0.37
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1412256; hg19: chr9-1464067;