rs4935720

Variant names:

• chr10-57762376-C-T
• rs4935720
• XR_001747454.1:n.86-60991G>A

Variant summary

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

The XR_001747454.1(LOC105378314):​n.86-60991G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 151,824 control chromosomes in the GnomAD database, including 47,896 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 0.79 (47896 hom., cov: 30)
• Consequence: LOC105378314 XR_001747454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417
• Publications: 1 publications found

Genes affected

LOC105378314 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.833 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: 0.791 AC: 120039 AN: 151706 Hom.: 47884 Cov.: 30

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.791 AC: 120089 AN: 151824 Hom.: 47896 Cov.: 30 AF XY: 0.787 AC XY: 58319 AN XY: 74146

African (AFR) AF: 0.713 AC: 29528 AN: 41398

American (AMR) AF: 0.845 AC: 12849 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3126 AN: 3468

East Asian (EAS) AF: 0.712 AC: 3651 AN: 5128

South Asian (SAS) AF: 0.604 AC: 2900 AN: 4804

European-Finnish (FIN) AF: 0.785 AC: 8294 AN: 10568

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56943 AN: 67932

Other (OTH) AF: 0.820 AC: 1730 AN: 2110

Alfa AF: 0.809 Hom.: 6482

Bravo AF: 0.799

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.40
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4935720; hg19: chr10-59522136;