XR_001747454.1:n.86-67628G>A

Variant names:

• chr10-57769013-C-T
• rs12358485
• XR_001747454.1:n.86-67628G>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.86-67628G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,864 control chromosomes in the GnomAD database, including 49,615 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 0.80 (49615 hom., cov: 32)
• Consequence: LOC105378314 XR_001747454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378314	XR_001747454.1	n.86-67628G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122088 AN: 151746 Hom.: 49603 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.804 AC: 122138 AN: 151864 Hom.: 49615 Cov.: 32 AF XY: 0.800 AC XY: 59382 AN XY: 74204

African (AFR) AF: 0.712 AC: 29520 AN: 41438

American (AMR) AF: 0.851 AC: 12937 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3165 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3671 AN: 5150

South Asian (SAS) AF: 0.606 AC: 2917 AN: 4814

European-Finnish (FIN) AF: 0.830 AC: 8785 AN: 10580

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

European-Non Finnish (NFE) AF: 0.859 AC: 58319 AN: 67894

Other (OTH) AF: 0.825 AC: 1739 AN: 2108

Alfa AF: 0.826 Hom.: 6769

Bravo AF: 0.809

Asia WGS AF: 0.630 AC: 2193 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.35
DANN	Benign	0.23
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12358485; hg19: chr10-59528773;