rs10186746

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-102249917-G-A
• chr2-102249917-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP144P2	XR_007087162.1	n.1311C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP144P2	ENST00000421987.1	n.339C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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;