rs4887052

Variant names:

• chr15-78411289-G-A
• rs4887052
• XR_932506.3:n.2935G>A

Variant summary

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

The XR_932506.3(LOC105370912):​n.2935G>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 0.189 in 152,122 control chromosomes in the GnomAD database, including 3,120 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 0.19 (3120 hom., cov: 32)
• Consequence: LOC105370912 XR_932506.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

LOC105370912 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28657 AN: 152004 Hom.: 3110 Cov.: 32

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.189 AC: 28689 AN: 152122 Hom.: 3120 Cov.: 32 AF XY: 0.191 AC XY: 14208 AN XY: 74380

African (AFR) AF: 0.0996 AC: 4136 AN: 41514

American (AMR) AF: 0.325 AC: 4955 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3472

East Asian (EAS) AF: 0.241 AC: 1245 AN: 5168

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4824

European-Finnish (FIN) AF: 0.190 AC: 2010 AN: 10578

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13484 AN: 67992

Other (OTH) AF: 0.218 AC: 460 AN: 2106

Alfa AF: 0.198 Hom.: 13667

Bravo AF: 0.192

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4887052; hg19: chr15-78703631;