12-92604738-A-G

Position:

• chr12-92604738-A-G

Variant summary

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

The XR_945211.3(LOC105369905):​n.316-24581A>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 0.0778 in 152,124 control chromosomes in the GnomAD database, including 482 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 0.078 (482 hom., cov: 32)
• Consequence: LOC105369905 XR_945211.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

LOC124902983 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902983	XR_007063406.1	n.222-6678T>C		intron_variant, non_coding_transcript_variant
LOC105369905	XR_945211.3	n.316-24581A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11838 AN: 152006 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0644

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

GnomAD4 genome AF: 0.0778 AC: 11836 AN: 152124 Hom.: 482 Cov.: 32 AF XY: 0.0781 AC XY: 5805 AN XY: 74360

Gnomad4 AFR AF: 0.0871

Gnomad4 AMR AF: 0.0502

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.0577

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.0637

Alfa AF: 0.0760 Hom.: 68

Bravo AF: 0.0716

Asia WGS AF: 0.0820 AC: 285 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17730330; hg19: chr12-92998514;