2-111618386-A-C

Position:

• chr2-111618386-A-C

Variant summary

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

The XR_001739641.2(LOC107985933):​n.1442T>G 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 0.677 in 152,106 control chromosomes in the GnomAD database, including 35,843 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 0.68 (35843 hom., cov: 33)
• Consequence: LOC107985933 XR_001739641.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

LOC107985933 (HGNC:):

ANAPC1 (HGNC:19988): (anaphase promoting complex subunit 1) This gene encodes a subunit of the anaphase-promoting complex. This complex is an E3 ubiquitin ligase that regulates progression through the metaphase to anaphase portion of the cell cycle by ubiquitinating proteins which targets them for degradation. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985933	XR_001739641.2	n.1442T>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000630717.1	n.27-18737A>C		intron_variant, non_coding_transcript_variant		5
ANAPC1	ENST00000643447.1	c.*140-3776T>G		intron_variant, NMD_transcript_variant				ENSP00000494863
	ENST00000645914.1	n.141-3776T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102862 AN: 151988 Hom.: 35820 Cov.: 33

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.677 AC: 102933 AN: 152106 Hom.: 35843 Cov.: 33 AF XY: 0.675 AC XY: 50169 AN XY: 74356

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.660

Alfa AF: 0.724 Hom.: 37595

Bravo AF: 0.663

Asia WGS AF: 0.462 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448190; hg19: chr2-112375963;