5-23056301-C-T

Variant names:

• chr5-23056301-C-T
• rs6879343
• XR_925849.2:n.180+17105C>T

Variant summary

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

The XR_925849.2(LOC105374686):​n.180+17105C>T 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 151,986 control chromosomes in the GnomAD database, including 1,633 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 (1633 hom., cov: 32)
• Consequence: LOC105374686 XR_925849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 publications found

Genes affected

LOC105374686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.143 AC: 21747 AN: 151868 Hom.: 1634 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.143 AC: 21760 AN: 151986 Hom.: 1633 Cov.: 32 AF XY: 0.142 AC XY: 10569 AN XY: 74274

African (AFR) AF: 0.160 AC: 6649 AN: 41450

American (AMR) AF: 0.0867 AC: 1324 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.148 AC: 765 AN: 5162

South Asian (SAS) AF: 0.119 AC: 573 AN: 4814

European-Finnish (FIN) AF: 0.173 AC: 1823 AN: 10558

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9791 AN: 67958

Other (OTH) AF: 0.115 AC: 242 AN: 2104

Alfa AF: 0.135 Hom.: 2521

Bravo AF: 0.139

Asia WGS AF: 0.118 AC: 409 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.077
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6879343; hg19: chr5-23056410;