rs6887595

Variant names:

• chr5-95632404-C-G
• rs6887595
• XR_002956221.2:n.-64G>C

Variant summary

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

The XR_002956221.2(LOC112267933):​n.-64G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,176 control chromosomes in the GnomAD database, including 1,624 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 0.12 (1624 hom., cov: 32)
• Consequence: LOC112267933 XR_002956221.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 3 publications found

Genes affected

LOC112267933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267933	XR_002956221.2	n.-64G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17568 AN: 152058 Hom.: 1607 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.116 AC: 17620 AN: 152176 Hom.: 1624 Cov.: 32 AF XY: 0.122 AC XY: 9057 AN XY: 74386

African (AFR) AF: 0.101 AC: 4201 AN: 41534

American (AMR) AF: 0.159 AC: 2423 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2879 AN: 5152

South Asian (SAS) AF: 0.142 AC: 687 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1358 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0806 AC: 5478 AN: 68004

Other (OTH) AF: 0.120 AC: 254 AN: 2114

Alfa AF: 0.0953 Hom.: 109

Bravo AF: 0.119

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs6887595; hg19: chr5-94968108;