rs387906400

Variant names:

• chr10-44378102-C-T
• rs387906400
• NM_199168.4:c.*531G>A

Variant summary

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

The NM_199168.4(CXCL12):​c.*531G>A variant causes a 3 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. Variant has been reported in ClinVar as protective (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CXCL12 NM_199168.4 3_prime_UTR
• Clinical Significance: protective no assertion criteria provided B:1
• Conservation: PhyloP100: -0.250
• Publications: 1 publications found

Genes affected

CXCL12 (HGNC:10672): (C-X-C motif chemokine ligand 12) This antimicrobial gene encodes a stromal cell-derived alpha chemokine member of the intercrine family. The encoded protein functions as the ligand for the G-protein coupled receptor, chemokine (C-X-C motif) receptor 4, and plays a role in many diverse cellular functions, including embryogenesis, immune surveillance, inflammation response, tissue homeostasis, and tumor growth and metastasis. Mutations in this gene are associated with resistance to human immunodeficiency virus type 1 infections. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

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=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199168.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL12	NM_199168.4	MANE Select	c.*531G>A		3_prime_UTR	Exon 3 of 3	NP_954637.1
	CXCL12	NM_001178134.2		c.267-197G>A		intron	N/A	NP_001171605.1
	CXCL12	NM_001033886.2		c.266+535G>A		intron	N/A	NP_001029058.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL12	ENST00000343575.11	TSL:1 MANE Select	c.*531G>A		3_prime_UTR	Exon 3 of 3	ENSP00000339913.6
	CXCL12	ENST00000395794.2	TSL:1	c.267-197G>A		intron	N/A	ENSP00000379140.2
	CXCL12	ENST00000374426.6	TSL:1	c.266+535G>A		intron	N/A	ENSP00000363548.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1294954 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 630692

African (AFR) AF: 0.00 AC: 0 AN: 28446

American (AMR) AF: 0.00 AC: 0 AN: 20588

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19538

East Asian (EAS) AF: 0.00 AC: 0 AN: 34712

South Asian (SAS) AF: 0.00 AC: 0 AN: 63714

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29958

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4834

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1039324

Other (OTH) AF: 0.00 AC: 0 AN: 53840

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions as Germline

Significance: protective

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Susceptibility to HIV infection (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs387906400; hg19: chr10-44873550;