rs12334460

chr8-9122179-T-C

Variant summary

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

The XR_007060803.1(LOC112268402):n.886+3786A>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 0.355 in 152,050 control chromosomes in the GnomAD database, including 10,184 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 0.36 (10184 hom., cov: 32)
• Consequence: LOC112268402 XR_007060803.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

LOC112268402 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268402	XR_007060803.1	n.886+3786A>G		intron_variant, non_coding_transcript_variant
LOC112268402	XR_007060804.1	n.887-3692A>G		intron_variant, non_coding_transcript_variant
LOC112268402	XR_007060805.1	n.813-382A>G		intron_variant, non_coding_transcript_variant
LOC112268402	XR_007060806.1	n.813-3692A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53981 AN: 151932 Hom.: 10182 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.355 AC: 53999 AN: 152050 Hom.: 10184 Cov.: 32 AF XY: 0.345 AC XY: 25678 AN XY: 74322

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.349

Alfa AF: 0.369 Hom.: 2388

Bravo AF: 0.358

Asia WGS AF: 0.196 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	5.4
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12334460; hg19: chr8-8979689;