rs2669849

Positions:

• chr3-39287383-T-C

Variant summary

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

The ENST00000605787.1(ADAD1P1):​n.1399T>C 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 0.157 in 152,222 control chromosomes in the GnomAD database, including 2,238 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 0.16 (2236 hom., cov: 32)
  • Exomes 𝑓: 0.30 (2 hom.)
• Consequence: ADAD1P1 ENST00000605787.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

ADAD1P1 (HGNC:44550): (adenosine deaminase domain containing 1 pseudogene 1)

CX3CR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CX3CR1	XM_047447538.1	c.-10+5409A>G		intron_variant			XP_047303494.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAD1P1	ENST00000605787.1	n.1399T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23837 AN: 152084 Hom.: 2235 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.300 AC: 6 AN: 20 Hom.: 2 Cov.: 0 AF XY: 0.278 AC XY: 5 AN XY: 18

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.214

GnomAD4 genome AF: 0.157 AC: 23843 AN: 152202 Hom.: 2236 Cov.: 32 AF XY: 0.151 AC XY: 11216 AN XY: 74422

Gnomad4 AFR AF: 0.0909

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.184

Alfa AF: 0.160 Hom.: 327

Bravo AF: 0.154

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2669849; hg19: chr3-39328874;