rs938203

Variant names:

• chr3-39281174-A-C
• rs938203
• NM_001171171.2:c.-141T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-39281174-A-C
• chr3-39281174-A-G
• chr3-39281174-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001171171.2(CX3CR1):​c.-141T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CX3CR1 NM_001171171.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 9 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001171171.2. 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
	CX3CR1	NM_001171171.2		c.-141T>G		5_prime_UTR	Exon 1 of 2	NP_001164642.1
	CX3CR1	NM_001171174.1		c.87+435T>G		intron	N/A	NP_001164645.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CX3CR1	ENST00000541347.5	TSL:4	c.-141T>G		5_prime_UTR	Exon 1 of 2	ENSP00000439140.1
	CX3CR1	ENST00000864857.1		c.-141T>G		5_prime_UTR	Exon 2 of 3	ENSP00000534916.1
	CX3CR1	ENST00000963325.1		c.-141T>G		5_prime_UTR	Exon 2 of 3	ENSP00000633384.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 863992 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 401226

African (AFR) AF: 0.00 AC: 0 AN: 16186

American (AMR) AF: 0.00 AC: 0 AN: 3156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5684

East Asian (EAS) AF: 0.00 AC: 0 AN: 4278

South Asian (SAS) AF: 0.00 AC: 0 AN: 21862

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1536

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1730

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 780622

Other (OTH) AF: 0.00 AC: 0 AN: 28938

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-0.53
PromoterAI		-0.027	Neutral

Splicing

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

Other links and lift over

dbSNP: rs938203; hg19: chr3-39322665;