10-121259506-T-C

Position:

• chr10-121259506-T-C

Variant summary

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

The XR_007062321.1(LOC105378523):​n.515+53710A>G 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 0.588 in 152,056 control chromosomes in the GnomAD database, including 26,705 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 0.59 (26705 hom., cov: 32)
• Consequence: LOC105378523 XR_007062321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

Genes affected

LOC105378523 (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 (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378523	XR_007062321.1	n.515+53710A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89290 AN: 151938 Hom.: 26688 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.588 AC: 89340 AN: 152056 Hom.: 26705 Cov.: 32 AF XY: 0.588 AC XY: 43722 AN XY: 74320

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.593

Alfa AF: 0.470 Hom.: 1614

Bravo AF: 0.583

Asia WGS AF: 0.693 AC: 2408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3925042; hg19: chr10-123019020;