rs10509535

chr10-88144674-A-G

Variant summary

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

The XR_001747537.3(LOC101929727):n.442+12121A>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 0.139 in 152,178 control chromosomes in the GnomAD database, including 2,361 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 0.14 (2361 hom., cov: 32)
• Consequence: LOC101929727 XR_001747537.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

Genes affected

LOC101929727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929727	XR_001747537.3	n.442+12121A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21068 AN: 152060 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.139 AC: 21093 AN: 152178 Hom.: 2361 Cov.: 32 AF XY: 0.135 AC XY: 10035 AN XY: 74404

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.0748

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0506

Gnomad4 NFE AF: 0.0681

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0843 Hom.: 528

Bravo AF: 0.147

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.82
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509535; hg19: chr10-89904431;