rs2816517

chr8-5920479-C-A

Variant summary

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

The XR_941375.2(LOC105377795):n.308-20748G>T 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 0.333 in 151,916 control chromosomes in the GnomAD database, including 8,973 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 0.33 (8973 hom., cov: 32)
• Consequence: LOC105377795 XR_941375.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

LOC105377795 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377795	XR_941375.2	n.308-20748G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50581 AN: 151800 Hom.: 8960 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.333 AC: 50630 AN: 151916 Hom.: 8973 Cov.: 32 AF XY: 0.335 AC XY: 24894 AN XY: 74264

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.353

Alfa AF: 0.376 Hom.: 11080

Bravo AF: 0.333

Asia WGS AF: 0.290 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.22
Dann	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2816517; hg19: chr8-5778001;