rs3844975

Variant names:

• chr15-87177480-A-G
• rs3844975
• XR_932582.2:n.167-747A>G

Variant summary

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

The XR_932582.2(LOC105370955):​n.167-747A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,904 control chromosomes in the GnomAD database, including 7,039 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 0.29 (7039 hom., cov: 31)
• Consequence: LOC105370955 XR_932582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 0 publications found

Genes affected

LOC105370955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 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: 0.290 AC: 43976 AN: 151784 Hom.: 7032 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.290 AC: 43998 AN: 151904 Hom.: 7039 Cov.: 31 AF XY: 0.292 AC XY: 21690 AN XY: 74224

African (AFR) AF: 0.149 AC: 6176 AN: 41486

American (AMR) AF: 0.405 AC: 6164 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1190 AN: 3464

East Asian (EAS) AF: 0.355 AC: 1824 AN: 5136

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4812

European-Finnish (FIN) AF: 0.378 AC: 3990 AN: 10552

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22551 AN: 67932

Other (OTH) AF: 0.293 AC: 616 AN: 2102

Alfa AF: 0.319 Hom.: 3427

Bravo AF: 0.286

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.64
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs3844975; hg19: chr15-87720711;