rs10841769

chr12-21242085-G-Achr12-21242085-G-C

Variant summary

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

The XR_007063239.1(LOC124902895):n.87-7786C>T 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 0.469 in 151,976 control chromosomes in the GnomAD database, including 17,123 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 0.47 (17123 hom., cov: 32)
• Consequence: LOC124902895 XR_007063239.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

Genes affected

LOC124902895 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902895	XR_007063239.1	n.87-7786C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71266 AN: 151858 Hom.: 17106 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.469 AC: 71327 AN: 151976 Hom.: 17123 Cov.: 32 AF XY: 0.474 AC XY: 35227 AN XY: 74256

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.480

Alfa AF: 0.466 Hom.: 16469

Bravo AF: 0.466

Asia WGS AF: 0.616 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	1.1
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10841769; hg19: chr12-21395019;