rs2645450

Variant names:

• chr8-11789003-T-C
• rs2645450
• XR_948962.4:n.44-936A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-11789003-T-C
• chr8-11789003-T-G

Variant summary

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

The XR_948962.4(LOC105379243):​n.44-936A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,972 control chromosomes in the GnomAD database, including 3,869 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 0.21 (3869 hom., cov: 31)
• Consequence: LOC105379243 XR_948962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 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: 0.213 AC: 32299 AN: 151852 Hom.: 3864 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.213 AC: 32318 AN: 151972 Hom.: 3869 Cov.: 31 AF XY: 0.220 AC XY: 16328 AN XY: 74270

African (AFR) AF: 0.102 AC: 4246 AN: 41482

American (AMR) AF: 0.290 AC: 4420 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3466

East Asian (EAS) AF: 0.240 AC: 1238 AN: 5156

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4810

European-Finnish (FIN) AF: 0.320 AC: 3378 AN: 10542

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16110 AN: 67956

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.199 Hom.: 1324

Bravo AF: 0.204

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2645450; hg19: chr8-11646512;