chr12-68686836-A-G

Position:

• chr12-68686836-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000433116.2(NUP107-DT):​n.2T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0718 in 564,686 control chromosomes in the GnomAD database, including 2,596 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.11 (1555 hom., cov: 33)
  • Exomes 𝑓: 0.058 (1041 hom.)
• Consequence: NUP107-DT ENST00000433116.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0790

Genes affected

NUP107-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 12-68686836-A-G is Benign according to our data. Variant chr12-68686836-A-G is described in ClinVar as [Benign]. Clinvar id is 1222965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507250	NR_038930.1	n.24T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUP107-DT	ENST00000502102.2	n.822+98T>C		intron_variant		1
NUP107-DT	ENST00000433116.2	n.2T>C		non_coding_transcript_exon_variant	1/2	2
NUP107-DT	ENST00000500695.2	n.24T>C		non_coding_transcript_exon_variant	1/3	5
NUP107-DT	ENST00000690517.1	n.41T>C		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16786 AN: 152214 Hom.: 1549 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0635

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0465

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0502

Gnomad OTH AF: 0.0841

GnomAD4 exome AF: 0.0575 AC: 23721 AN: 412354 Hom.: 1041 Cov.: 4 AF XY: 0.0561 AC XY: 12168 AN XY: 216716

Gnomad4 AFR exome AF: 0.245

Gnomad4 AMR exome AF: 0.0564

Gnomad4 ASJ exome AF: 0.0457

Gnomad4 EAS exome AF: 0.0000685

Gnomad4 SAS exome AF: 0.0516

Gnomad4 FIN exome AF: 0.111

Gnomad4 NFE exome AF: 0.0501

Gnomad4 OTH exome AF: 0.0658

GnomAD4 genome AF: 0.110 AC: 16820 AN: 152332 Hom.: 1555 Cov.: 33 AF XY: 0.111 AC XY: 8288 AN XY: 74488

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0462

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0502

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0591 Hom.: 423

Bravo AF: 0.111

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 20, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.3
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12831591; hg19: chr12-69080616;