rs16954462

Variant names:

• chr13-87399205-G-A
• rs16954462
• XR_931625.3:n.486-24291G>A

Variant summary

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

The XR_931625.3(LOC105370302):​n.486-24291G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 152,154 control chromosomes in the GnomAD database, including 200 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 0.038 (200 hom., cov: 32)
• Consequence: LOC105370302 XR_931625.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

LOC105370302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370302	XR_931625.3	n.486-24291G>A		intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5750 AN: 152036 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.00434

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0379 AC: 5770 AN: 152154 Hom.: 200 Cov.: 32 AF XY: 0.0376 AC XY: 2801 AN XY: 74396

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.0294

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0174

Gnomad4 FIN AF: 0.00434

Gnomad4 NFE AF: 0.0166

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0253 Hom.: 62

Bravo AF: 0.0422

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16954462; hg19: chr13-88051460;