3-39287383-T-C

Variant names:

• chr3-39287383-T-C
• rs2669849
• XM_047447538.1:c.-10+5409A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

CX3CR1 (HGNC:2558): (C-X3-C motif chemokine receptor 1) Fractalkine is a transmembrane protein and chemokine involved in the adhesion and migration of leukocytes. The protein encoded by this gene is a receptor for fractalkine. The encoded protein also is a coreceptor for HIV-1, and some variations in this gene lead to increased susceptibility to HIV-1 infection and rapid progression to AIDS. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605787.1. 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
	ADAD1P1	ENST00000605787.1	TSL:6	n.1399T>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0909 AC: 3775 AN: 41540

American (AMR) AF: 0.151 AC: 2302 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3466

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5184

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4824

European-Finnish (FIN) AF: 0.143 AC: 1518 AN: 10598

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14624 AN: 68002

Other (OTH) AF: 0.184 AC: 389 AN: 2114

Alfa AF: 0.158 Hom.: 335

Bravo AF: 0.154

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs2669849; hg19: chr3-39328874;