chr10-44385487-G-A

Position:

• chr10-44385487-G-A

Variant summary

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

The variant allele was found at a frequency of 0.0847 in 152,282 control chromosomes in the GnomAD database, including 759 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 0.085 (759 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44385487G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXCL12	ENST00000496375.1	n.518+489C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0848 AC: 12908 AN: 152164 Hom.: 759 Cov.: 33

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0900

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0847 AC: 12905 AN: 152282 Hom.: 759 Cov.: 33 AF XY: 0.0824 AC XY: 6131 AN XY: 74450

Gnomad4 AFR AF: 0.0228

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0180

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.0969 Hom.: 168

Bravo AF: 0.0806

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17880313; hg19: chr10-44880935;