XR_001747453.1:n.484-10246A>C

Variant names:

• chr10-57332922-T-G
• rs12244977
• XR_001747453.1:n.484-10246A>C

Variant summary

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

The XR_001747453.1(LOC105378313):​n.484-10246A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,942 control chromosomes in the GnomAD database, including 3,702 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 0.16 (3702 hom., cov: 31)
• Consequence: LOC105378313 XR_001747453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 4 publications found

Genes affected

LOC105378313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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: 0.157 AC: 23875 AN: 151824 Hom.: 3691 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.158 AC: 23940 AN: 151942 Hom.: 3702 Cov.: 31 AF XY: 0.158 AC XY: 11735 AN XY: 74270

African (AFR) AF: 0.396 AC: 16365 AN: 41372

American (AMR) AF: 0.207 AC: 3154 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0453 AC: 157 AN: 3468

East Asian (EAS) AF: 0.0938 AC: 483 AN: 5148

South Asian (SAS) AF: 0.0851 AC: 410 AN: 4818

European-Finnish (FIN) AF: 0.0292 AC: 309 AN: 10598

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0401 AC: 2723 AN: 67980

Other (OTH) AF: 0.135 AC: 286 AN: 2114

Alfa AF: 0.0731 Hom.: 564

Bravo AF: 0.182

Asia WGS AF: 0.127 AC: 442 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	0.71
DANN	Benign	0.36
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs12244977; hg19: chr10-59092682;