rs10502519

chr18-29245022-T-G

Variant summary

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

The XR_935327.3(LOC105372044):n.70-8297A>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 0.0616 in 152,260 control chromosomes in the GnomAD database, including 314 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 0.062 (314 hom., cov: 32)
• Consequence: LOC105372044 XR_935327.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

Genes affected

LOC105372044 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372044	XR_935327.3	n.70-8297A>C		intron_variant, non_coding_transcript_variant
LOC105372044	XR_935328.2	n.61-8297A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9356 AN: 152142 Hom.: 314 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0616 AC: 9377 AN: 152260 Hom.: 314 Cov.: 32 AF XY: 0.0606 AC XY: 4510 AN XY: 74450

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.0958

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.0780

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0738

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0633 Hom.: 40

Bravo AF: 0.0632

Asia WGS AF: 0.0570 AC: 199 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.2
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502519; hg19: chr18-26824987;