XR_007065537.1:n.282+8349T>G

Variant names:

• chr1-23560444-T-G
• rs1555025
• XR_007065537.1:n.282+8349T>G

Variant summary

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

The XR_007065537.1(LOC124903876):​n.282+8349T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 150,996 control chromosomes in the GnomAD database, including 23,883 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 0.56 (23883 hom., cov: 28)
• Consequence: LOC124903876 XR_007065537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

Genes affected

LOC124903876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903876	XR_007065537.1	n.282+8349T>G		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84269 AN: 150880 Hom.: 23851 Cov.: 28

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.559 AC: 84358 AN: 150996 Hom.: 23883 Cov.: 28 AF XY: 0.556 AC XY: 41010 AN XY: 73700

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.561

Alfa AF: 0.536 Hom.: 20273

Bravo AF: 0.564

Asia WGS AF: 0.559 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555025; hg19: chr1-23886935; COSMIC: COSV65800882;