rs16947390

chr16-49418176-T-C

Variant summary

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

The XR_001752167.2(LOC105371244):n.1284-3287A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,194 control chromosomes in the GnomAD database, including 635 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 0.074 (635 hom., cov: 32)
• Consequence: LOC105371244 XR_001752167.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

Genes affected

LOC105371244 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371244	XR_001752167.2	n.1284-3287A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11189 AN: 152076 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0736 AC: 11199 AN: 152194 Hom.: 635 Cov.: 32 AF XY: 0.0707 AC XY: 5264 AN XY: 74406

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.0346

Gnomad4 SAS AF: 0.0820

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0643 Hom.: 69

Bravo AF: 0.0768

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.54
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16947390; hg19: chr16-49452087;