10-58466175-A-G

Variant names:

• chr10-58466175-A-G
• rs2114561
• XR_007062374.1:n.96-1010A>G

Variant summary

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

The XR_945981.3(LOC105378316):​n.361-1010A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,078 control chromosomes in the GnomAD database, including 37,026 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 0.69 (37026 hom., cov: 32)
• Consequence: LOC105378316 XR_945981.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

LOC105378316 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.96-1010A>G		intron_variant	Intron 1 of 3
LOC105378316	XR_945981.3	n.361-1010A>G		intron_variant	Intron 2 of 5
LOC105378316	XR_945982.3	n.361-1010A>G		intron_variant	Intron 2 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104736 AN: 151960 Hom.: 37013 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.689 AC: 104788 AN: 152078 Hom.: 37026 Cov.: 32 AF XY: 0.687 AC XY: 51101 AN XY: 74330

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.676

Alfa AF: 0.754 Hom.: 42161

Bravo AF: 0.689

Asia WGS AF: 0.621 AC: 2160 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2114561; hg19: chr10-60225935;