rs10101364

Variant names:

• chr8-20777377-C-T
• rs10101364
• XR_949569.4:n.72-13069C>T

Variant summary

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

The XR_949569.4(LOC105379315):​n.72-13069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,080 control chromosomes in the GnomAD database, including 41,805 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 0.74 (41805 hom., cov: 33)
• Consequence: LOC105379315 XR_949569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 4 publications found

Genes affected

LOC105379315 (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 (EAS) allele frequency at 95% confidence interval = 0.957 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: 0.737 AC: 112004 AN: 151960 Hom.: 41764 Cov.: 33

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.737 AC: 112101 AN: 152080 Hom.: 41805 Cov.: 33 AF XY: 0.737 AC XY: 54773 AN XY: 74318

African (AFR) AF: 0.806 AC: 33443 AN: 41486

American (AMR) AF: 0.796 AC: 12146 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2707 AN: 3468

East Asian (EAS) AF: 0.979 AC: 5079 AN: 5186

South Asian (SAS) AF: 0.800 AC: 3855 AN: 4820

European-Finnish (FIN) AF: 0.595 AC: 6277 AN: 10546

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46276 AN: 67988

Other (OTH) AF: 0.750 AC: 1587 AN: 2116

Alfa AF: 0.706 Hom.: 22593

Bravo AF: 0.758

Asia WGS AF: 0.864 AC: 3005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.63
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10101364; hg19: chr8-20634888;