XR_001752339.2:n.381+880C>T

Variant names:

• chr16-15947911-G-A
• rs4148330
• XR_001752339.2:n.381+880C>T

Variant summary

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

The XR_001752339.2(LOC107984869):​n.381+880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,956 control chromosomes in the GnomAD database, including 26,235 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 0.57 (26235 hom., cov: 31)
• Consequence: LOC107984869 XR_001752339.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 11 publications found

Genes affected

LOC107984869 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.683 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: 0.567 AC: 86149 AN: 151836 Hom.: 26216 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.567 AC: 86207 AN: 151956 Hom.: 26235 Cov.: 31 AF XY: 0.565 AC XY: 41963 AN XY: 74272

African (AFR) AF: 0.333 AC: 13800 AN: 41420

American (AMR) AF: 0.567 AC: 8645 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2187 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3072 AN: 5154

South Asian (SAS) AF: 0.605 AC: 2908 AN: 4810

European-Finnish (FIN) AF: 0.659 AC: 6948 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46809 AN: 67988

Other (OTH) AF: 0.584 AC: 1229 AN: 2106

Alfa AF: 0.630 Hom.: 82418

Bravo AF: 0.546

Asia WGS AF: 0.588 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs4148330; hg19: chr16-16041768;