12-115518124-C-T

Position:

• chr12-115518124-C-T

Variant summary

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

The XR_945389.3(LOC105370003):​n.119-9710G>A 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 0.133 in 152,084 control chromosomes in the GnomAD database, including 3,265 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 0.13 (3265 hom., cov: 33)
• Consequence: LOC105370003 XR_945389.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

LOC105370003 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370003	XR_945389.3	n.119-9710G>A		intron_variant, non_coding_transcript_variant
LOC105370003	XR_945388.3	n.119-9710G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20206 AN: 151966 Hom.: 3252 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.00705

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.133 AC: 20261 AN: 152084 Hom.: 3265 Cov.: 33 AF XY: 0.128 AC XY: 9482 AN XY: 74368

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.00685

Gnomad4 FIN AF: 0.0355

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0939 Hom.: 269

Bravo AF: 0.148

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7134205; hg19: chr12-115955929;