12-97245366-A-G

Position:

• chr12-97245366-A-G

Variant summary

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

The XR_246024.4(LOC101928912):​n.223+7402T>C 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 0.669 in 517,280 control chromosomes in the GnomAD database, including 118,212 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 0.64 (32297 hom., cov: 32)
  • Exomes 𝑓: 0.68 (85915 hom.)
• Consequence: LOC101928912 XR_246024.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.801

Genes affected

LOC101928912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928912	XR_246024.4	n.223+7402T>C		intron_variant, non_coding_transcript_variant
LOC101928912	XR_945251.3	n.224-1644T>C		intron_variant, non_coding_transcript_variant
LOC101928912	XR_945252.3	n.224-4304T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97551 AN: 151756 Hom.: 32292 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.692

GnomAD3 exomes AF: 0.677 AC: 154159 AN: 227740 Hom.: 53097 AF XY: 0.677 AC XY: 85206 AN XY: 125942

Gnomad AFR exome AF: 0.473

Gnomad AMR exome AF: 0.668

Gnomad ASJ exome AF: 0.793

Gnomad EAS exome AF: 0.672

Gnomad SAS exome AF: 0.551

Gnomad FIN exome AF: 0.685

Gnomad NFE exome AF: 0.730

Gnomad OTH exome AF: 0.707

GnomAD4 exome AF: 0.680 AC: 248546 AN: 365406 Hom.: 85915 Cov.: 0 AF XY: 0.671 AC XY: 140734 AN XY: 209604

Gnomad4 AFR exome AF: 0.474

Gnomad4 AMR exome AF: 0.669

Gnomad4 ASJ exome AF: 0.798

Gnomad4 EAS exome AF: 0.678

Gnomad4 SAS exome AF: 0.556

Gnomad4 FIN exome AF: 0.694

Gnomad4 NFE exome AF: 0.726

Gnomad4 OTH exome AF: 0.705

GnomAD4 genome AF: 0.643 AC: 97601 AN: 151874 Hom.: 32297 Cov.: 32 AF XY: 0.641 AC XY: 47597 AN XY: 74206

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.690

Alfa AF: 0.719 Hom.: 92959

Bravo AF: 0.641

Asia WGS AF: 0.566 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	15
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012315; hg19: chr12-97639144; COSMIC: COSV67304688;