XR_001748217.1:n.1008-3735T>C

Variant names:

• chr11-57198500-A-G
• rs10501365
• XR_001748217.1:n.1008-3735T>C

Variant summary

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

The XR_001748217.1(LOC105369309):​n.1008-3735T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,286 control chromosomes in the GnomAD database, including 1,067 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 0.11 (1067 hom., cov: 32)
• Consequence: LOC105369309 XR_001748217.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75
• Publications: 3 publications found

Genes affected

LOC105369309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16917 AN: 152168 Hom.: 1070 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.111 AC: 16920 AN: 152286 Hom.: 1067 Cov.: 32 AF XY: 0.111 AC XY: 8287 AN XY: 74456

African (AFR) AF: 0.109 AC: 4548 AN: 41552

American (AMR) AF: 0.133 AC: 2040 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 294 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1429 AN: 5170

South Asian (SAS) AF: 0.0928 AC: 448 AN: 4830

European-Finnish (FIN) AF: 0.0569 AC: 604 AN: 10612

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7227 AN: 68032

Other (OTH) AF: 0.104 AC: 221 AN: 2116

Alfa AF: 0.111 Hom.: 2061

Bravo AF: 0.120

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.77
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs10501365; hg19: chr11-56965974;