12-69723466-C-T

Position:

• chr12-69723466-C-T

Variant summary

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

The NR_110072.2(LOC101928002):​n.565+1756G>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 0.349 in 151,872 control chromosomes in the GnomAD database, including 9,459 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 (9459 hom., cov: 31)
• Consequence: LOC101928002 NR_110072.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928002	NR_110072.2	n.565+1756G>A		intron_variant, non_coding_transcript_variant
LOC101928002	NR_159971.1	n.442-895G>A		intron_variant, non_coding_transcript_variant
LOC101928002	NR_159972.1	n.441+1756G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000501387.6	n.589+1756G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000501300.1	n.454-895G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000661191.1	n.441+1756G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52906 AN: 151754 Hom.: 9452 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.349 AC: 52937 AN: 151872 Hom.: 9459 Cov.: 31 AF XY: 0.351 AC XY: 26030 AN XY: 74198

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.325

Alfa AF: 0.357 Hom.: 13172

Bravo AF: 0.334

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.047
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs775450; hg19: chr12-70117246;