rs10186746

Positions:

• chr2-102249917-G-A
• chr2-102249917-G-T

Variant summary

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

The ENST00000421987.1(FAM183DP):​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: FAM183DP ENST00000421987.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581

Genes affected

FAM183DP (HGNC:51331): (CFAP144 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FAM183DP	XR_007087162.1	n.1311C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM183DP	ENST00000421987.1	n.339C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.142

Gnomad4 AMR exome AF: 0.161

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.549

Gnomad4 SAS exome AF: 0.468

Gnomad4 FIN exome AF: 0.381

Gnomad4 NFE exome AF: 0.290

Gnomad4 OTH exome AF: 0.314

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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.333

Alfa AF: 0.347 Hom.: 1202

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10186746; hg19: chr2-102866377;