ENST00000421987.1:n.339C>T

Variant names:

• chr2-102249917-G-A
• rs10186746
• ENST00000421987.1:n.339C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421987.1(CFAP144P2):​n.339C>T 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 0.331 in 213,444 control chromosomes in the GnomAD database, including 12,906 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 0.34 (9567 hom., cov: 33)
  • Exomes 𝑓: 0.31 (3339 hom.)
• Consequence: CFAP144P2 ENST00000421987.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 6 publications found

Genes affected

CFAP144P2 (HGNC:51331): (CFAP144 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421987.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP144P2	ENST00000421987.1	TSL:6	n.339C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51442 AN: 151830 Hom.: 9578 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.313 AC: 19255 AN: 61494 Hom.: 3339 Cov.: 0 AF XY: 0.319 AC XY: 11099 AN XY: 34770

African (AFR) AF: 0.142 AC: 220 AN: 1552

American (AMR) AF: 0.161 AC: 879 AN: 5458

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 240 AN: 1246

East Asian (EAS) AF: 0.549 AC: 1050 AN: 1912

South Asian (SAS) AF: 0.468 AC: 3441 AN: 7352

European-Finnish (FIN) AF: 0.381 AC: 2590 AN: 6790

Middle Eastern (MID) AF: 0.229 AC: 48 AN: 210

European-Non Finnish (NFE) AF: 0.290 AC: 9864 AN: 34032

Other (OTH) AF: 0.314 AC: 923 AN: 2942

GnomAD4 genome AF: 0.339 AC: 51444 AN: 151950 Hom.: 9567 Cov.: 33 AF XY: 0.347 AC XY: 25737 AN XY: 74272

African (AFR) AF: 0.230 AC: 9510 AN: 41402

American (AMR) AF: 0.298 AC: 4555 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3447 AN: 5134

South Asian (SAS) AF: 0.594 AC: 2865 AN: 4824

European-Finnish (FIN) AF: 0.417 AC: 4407 AN: 10558

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24703 AN: 67970

Other (OTH) AF: 0.333 AC: 703 AN: 2112

Alfa AF: 0.342 Hom.: 1220

Bravo AF: 0.320

Asia WGS AF: 0.617 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.65
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs10186746; hg19: chr2-102866377;