chr10-57805368-A-T

Variant names:

• chr10-57805368-A-T
• rs1505918
• XR_001747454.1:n.85+41924T>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.85+41924T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 151,984 control chromosomes in the GnomAD database, including 50,038 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 0.81 (50038 hom., cov: 31)
• Consequence: LOC105378314 XR_001747454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 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: 0.807 AC: 122620 AN: 151866 Hom.: 50028 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.807 AC: 122669 AN: 151984 Hom.: 50038 Cov.: 31 AF XY: 0.803 AC XY: 59604 AN XY: 74268

African (AFR) AF: 0.714 AC: 29609 AN: 41470

American (AMR) AF: 0.851 AC: 12954 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3163 AN: 3470

East Asian (EAS) AF: 0.714 AC: 3649 AN: 5114

South Asian (SAS) AF: 0.581 AC: 2800 AN: 4816

European-Finnish (FIN) AF: 0.833 AC: 8814 AN: 10578

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58829 AN: 67988

Other (OTH) AF: 0.828 AC: 1751 AN: 2114

Alfa AF: 0.833 Hom.: 6589

Bravo AF: 0.812

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.77
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1505918; hg19: chr10-59565128;