rs3844975

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105370955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370955	XR_932582.2	n.167-747A>G		intron_variant	Intron 2 of 2

Ensembl

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

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

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.293

Alfa AF: 0.324 Hom.: 2911

Bravo AF: 0.286

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3844975; hg19: chr15-87720711;