4-134616564-T-C

Variant names:

• chr4-134616564-T-C
• rs6535028
• XR_939214.2:n.393-23016T>C

Variant summary

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

The XR_939214.2(LOC105377436):​n.393-23016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,114 control chromosomes in the GnomAD database, including 62,061 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 0.90 (62061 hom., cov: 33)
• Consequence: LOC105377436 XR_939214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 7 publications found

Genes affected

LOC105377436 (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 (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.903 AC: 137193 AN: 151996 Hom.: 62018 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.903 AC: 137292 AN: 152114 Hom.: 62061 Cov.: 33 AF XY: 0.905 AC XY: 67304 AN XY: 74368

African (AFR) AF: 0.854 AC: 35476 AN: 41546

American (AMR) AF: 0.938 AC: 14340 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2997 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5177 AN: 5180

South Asian (SAS) AF: 0.942 AC: 4548 AN: 4830

European-Finnish (FIN) AF: 0.924 AC: 9782 AN: 10592

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

European-Non Finnish (NFE) AF: 0.912 AC: 61954 AN: 67896

Other (OTH) AF: 0.912 AC: 1924 AN: 2110

Alfa AF: 0.910 Hom.: 86917

Bravo AF: 0.901

Asia WGS AF: 0.962 AC: 3336 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.66
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6535028; hg19: chr4-135537719;