rs2645444

Variant names:

• chr8-11794044-C-T
• rs2645444
• XR_948962.4:n.44-5977G>A

Variant summary

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

The XR_948962.4(LOC105379243):​n.44-5977G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 151,998 control chromosomes in the GnomAD database, including 50,632 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 0.81 (50632 hom., cov: 31)
• Consequence: LOC105379243 XR_948962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 8 publications found

Genes affected

LOC105379243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.815 AC: 123715 AN: 151880 Hom.: 50578 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.815 AC: 123827 AN: 151998 Hom.: 50632 Cov.: 31 AF XY: 0.819 AC XY: 60835 AN XY: 74294

African (AFR) AF: 0.779 AC: 32254 AN: 41414

American (AMR) AF: 0.873 AC: 13348 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5146 AN: 5168

South Asian (SAS) AF: 0.844 AC: 4069 AN: 4820

European-Finnish (FIN) AF: 0.836 AC: 8835 AN: 10570

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54962 AN: 67966

Other (OTH) AF: 0.821 AC: 1727 AN: 2104

Alfa AF: 0.814 Hom.: 87025

Bravo AF: 0.815

Asia WGS AF: 0.925 AC: 3212 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	0.37
DANN	Benign	0.25
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs2645444; hg19: chr8-11651553;