rs10507632

chr13-59520528-T-C

Variant summary

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

The XR_001749886.2(LOC107984625):n.358-783A>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 0.111 in 152,240 control chromosomes in the GnomAD database, including 2,016 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 0.11 (2016 hom., cov: 32)
• Consequence: LOC107984625 XR_001749886.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

Genes affected

LOC107984625 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984625	XR_001749886.2	n.358-783A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16917 AN: 152122 Hom.: 2012 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.111 AC: 16937 AN: 152240 Hom.: 2016 Cov.: 32 AF XY: 0.109 AC XY: 8123 AN XY: 74464

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.0704

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00675

Gnomad4 SAS AF: 0.0689

Gnomad4 FIN AF: 0.0340

Gnomad4 NFE AF: 0.0306

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0706 Hom.: 497

Bravo AF: 0.122

Asia WGS AF: 0.0570 AC: 198 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	5.0
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507632; hg19: chr13-60094662;