XR_001745898.2:n.886+2206T>C

Variant names:

• chr8-52772301-T-C
• rs7822058
• XR_001745898.2:n.886+2206T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745898.2(LOC105375835):​n.886+2206T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,222 control chromosomes in the GnomAD database, including 61,069 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 0.90 (61069 hom., cov: 32)
• Consequence: LOC105375835 XR_001745898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

LOC105375835 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375835	XR_001745898.2	n.886+2206T>C		intron_variant	Intron 5 of 6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136217 AN: 152104 Hom.: 61006 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.896 AC: 136339 AN: 152222 Hom.: 61069 Cov.: 32 AF XY: 0.898 AC XY: 66806 AN XY: 74430

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.899

Alfa AF: 0.890 Hom.: 76438

Bravo AF: 0.900

Asia WGS AF: 0.934 AC: 3248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7822058; hg19: chr8-53684861;