12-131252268-C-T

Position:

• chr12-131252268-C-T

Variant summary

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

The XR_945559.3(LOC105370082):​n.728+9107G>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 0.351 in 151,960 control chromosomes in the GnomAD database, including 10,827 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 0.35 (10827 hom., cov: 32)
• Consequence: LOC105370082 XR_945559.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

LOC105370082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370082	XR_945559.3	n.728+9107G>A		intron_variant, non_coding_transcript_variant
LOC105370082	XR_945558.3	n.890+9107G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53316 AN: 151842 Hom.: 10830 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.351 AC: 53307 AN: 151960 Hom.: 10827 Cov.: 32 AF XY: 0.357 AC XY: 26484 AN XY: 74268

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.359

Alfa AF: 0.393 Hom.: 16088

Bravo AF: 0.328

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.3
CADD	Benign	0.18
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4759885; hg19: chr12-131736813;