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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986891	XR_001745719.1	n.165+17159C>T		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;