rs10824804

Positions:

• chr10-52793045-A-C
• chr10-52793045-A-G

Variant summary

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

The XR_945963.2(LOC105378306):​n.507+2727A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,768 control chromosomes in the GnomAD database, including 13,080 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 0.41 (13080 hom., cov: 31)
• Consequence: LOC105378306 XR_945963.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

LOC105378306 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378306	XR_945963.2	n.507+2727A>C		intron_variant, non_coding_transcript_variant
LOC105378307	XR_945965.3	n.370-8711T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61594 AN: 151650 Hom.: 13086 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.406 AC: 61581 AN: 151768 Hom.: 13080 Cov.: 31 AF XY: 0.407 AC XY: 30148 AN XY: 74164

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.427

Alfa AF: 0.459 Hom.: 23560

Bravo AF: 0.392

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10824804; hg19: chr10-54552805;