chr5-103929013-C-T

Variant names:

• chr5-103929013-C-T
• rs811132
• XR_001742830.2:n.352-4552C>T

Variant summary

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

The XR_001742830.2(LOC105379107):​n.352-4552C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,170 control chromosomes in the GnomAD database, including 58,531 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 0.88 (58531 hom., cov: 32)
• Consequence: LOC105379107 XR_001742830.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 2 publications found

Genes affected

LOC105379107 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.875 AC: 133114 AN: 152052 Hom.: 58497 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.875 AC: 133204 AN: 152170 Hom.: 58531 Cov.: 32 AF XY: 0.879 AC XY: 65363 AN XY: 74402

African (AFR) AF: 0.805 AC: 33417 AN: 41500

American (AMR) AF: 0.891 AC: 13612 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3158 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5142 AN: 5172

South Asian (SAS) AF: 0.924 AC: 4459 AN: 4826

European-Finnish (FIN) AF: 0.944 AC: 10009 AN: 10602

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60560 AN: 68012

Other (OTH) AF: 0.876 AC: 1844 AN: 2106

Alfa AF: 0.890 Hom.: 7496

Bravo AF: 0.867

Asia WGS AF: 0.955 AC: 3320 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs811132; hg19: chr5-103264714; COSMIC: COSV60175803;