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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378314	XR_001747454.1	n.86-60991G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;