rs16938588

Positions:

• chr8-73184479-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.73184479G>A		intergenic_region
LOC107986891	XR_001745719.1	n.165+17159C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.153

Alfa AF: 0.137 Hom.: 220

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16938588; hg19: chr8-74096714;