2-87719965-C-G

Variant names:

• chr2-87719965-C-G
• rs576510766
• ENST00000427434.2:n.1078C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_160651.1(ANAPC1P4):​n.1013C>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 0.0000162 in 1,540,778 control chromosomes in the GnomAD database, including 1 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 0.000042 (1 hom., cov: 22)
  • Exomes 𝑓: 0.000014 (0 hom.)
• Consequence: ANAPC1P4 NR_160651.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 0 publications found

Genes affected

ANAPC1P4 (HGNC:54710): (ANAPC1 pseudogene 4)

NCAL1 (HGNC:56663): (NK cell activity associated lncRNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_160651.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANAPC1P4	NR_160651.1		n.1013C>G		non_coding_transcript_exon	Exon 8 of 15
	NCAL1	NR_186253.1		n.1331C>G		non_coding_transcript_exon	Exon 10 of 15

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANAPC1P4	ENST00000427434.2	TSL:6	n.1078C>G		non_coding_transcript_exon	Exon 9 of 15
	NCAL1	ENST00000643276.1		n.1448C>G		non_coding_transcript_exon	Exon 11 of 18
	NCAL1	ENST00000646855.1		n.1322C>G		non_coding_transcript_exon	Exon 10 of 22

Frequencies

GnomAD3 genomes AF: 0.0000424 AC: 6 AN: 141474 Hom.: 1 Cov.: 22

Gnomad AFR AF: 0.0000833

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000690

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000153

Gnomad OTH AF: 0.000525

GnomAD4 exome AF: 0.0000136 AC: 19 AN: 1399304 Hom.: 0 Cov.: 27 AF XY: 0.0000100 AC XY: 7 AN XY: 697026

African (AFR) AF: 0.00 AC: 0 AN: 30734

American (AMR) AF: 0.00 AC: 0 AN: 43814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25198

East Asian (EAS) AF: 0.00 AC: 0 AN: 39000

South Asian (SAS) AF: 0.00 AC: 0 AN: 82556

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50746

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4306

European-Non Finnish (NFE) AF: 0.0000160 AC: 17 AN: 1064904

Other (OTH) AF: 0.0000345 AC: 2 AN: 58046

GnomAD4 genome AF: 0.0000424 AC: 6 AN: 141474 Hom.: 1 Cov.: 22 AF XY: 0.0000291 AC XY: 2 AN XY: 68652

African (AFR) AF: 0.0000833 AC: 3 AN: 36036

American (AMR) AF: 0.0000690 AC: 1 AN: 14494

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3322

East Asian (EAS) AF: 0.00 AC: 0 AN: 4930

South Asian (SAS) AF: 0.00 AC: 0 AN: 4188

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9898

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 300

European-Non Finnish (NFE) AF: 0.0000153 AC: 1 AN: 65520

Other (OTH) AF: 0.000525 AC: 1 AN: 1904

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000718

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	0.86
DANN	Benign	0.78
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs576510766; hg19: chr2-88019484;