rs16938588

Variant names:

• chr8-73184479-G-A
• rs16938588
• XR_001745719.1:n.165+17159C>T

Variant summary

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

The XR_001745719.1(LOC107986891):​n.165+17159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,134 control chromosomes in the GnomAD database, including 1,630 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 0.13 (1630 hom., cov: 32)
• Consequence: LOC107986891 XR_001745719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 6 publications found

Genes affected

LOC107986891 (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 (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19486 AN: 152016 Hom.: 1637 Cov.: 32

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.128 AC: 19478 AN: 152134 Hom.: 1630 Cov.: 32 AF XY: 0.130 AC XY: 9683 AN XY: 74368

African (AFR) AF: 0.0431 AC: 1789 AN: 41494

American (AMR) AF: 0.177 AC: 2710 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 744 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1892 AN: 5174

South Asian (SAS) AF: 0.156 AC: 750 AN: 4820

European-Finnish (FIN) AF: 0.129 AC: 1368 AN: 10568

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9729 AN: 68002

Other (OTH) AF: 0.153 AC: 322 AN: 2110

Alfa AF: 0.135 Hom.: 223

Bravo AF: 0.133

Asia WGS AF: 0.214 AC: 745 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	2.6
DANN	Benign	0.61
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs16938588; hg19: chr8-74096714;