10-44386212-C-T

Variant names:

• chr10-44386212-C-T
• rs17885289
• ENST00000496375.1:n.282G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000496375.1(CXCL12):​n.282G>A 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 0.259 in 152,234 control chromosomes in the GnomAD database, including 5,348 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 0.26 (5336 hom., cov: 32)
  • Exomes 𝑓: 0.32 (12 hom.)
• Consequence: CXCL12 ENST00000496375.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 5 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]

ENSG00000303087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000496375.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CXCL12	ENST00000496375.1	TSL:5	n.282G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000303087	ENST00000791650.1		n.51+2036C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39402 AN: 151924 Hom.: 5336 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.272

GnomAD4 exome AF: 0.318 AC: 61 AN: 192 Hom.: 12 Cov.: 0 AF XY: 0.331 AC XY: 47 AN XY: 142

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.167 AC: 1 AN: 6

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.333 AC: 56 AN: 168

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.259 AC: 39407 AN: 152042 Hom.: 5336 Cov.: 32 AF XY: 0.255 AC XY: 18952 AN XY: 74300

African (AFR) AF: 0.226 AC: 9381 AN: 41510

American (AMR) AF: 0.226 AC: 3451 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3472

East Asian (EAS) AF: 0.0966 AC: 494 AN: 5116

South Asian (SAS) AF: 0.120 AC: 577 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3104 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20719 AN: 67946

Other (OTH) AF: 0.269 AC: 565 AN: 2102

Alfa AF: 0.181 Hom.: 402

Bravo AF: 0.254

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.4
DANN	Benign	0.74
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs17885289; hg19: chr10-44881660;