13-46761855-A-G

Variant names:

• chr13-46761855-A-G
• rs7996797
• XR_001749983.2:n.*223A>G

Variant summary

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

The XR_001749983.2(LOC107984563):​n.*223A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,030 control chromosomes in the GnomAD database, including 12,398 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 0.40 (12398 hom., cov: 32)
• Consequence: LOC107984563 XR_001749983.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

Genes affected

LOC107984563 (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 (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984563	XR_001749983.2	n.*223A>G		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60763 AN: 151912 Hom.: 12394 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.400 AC: 60802 AN: 152030 Hom.: 12398 Cov.: 32 AF XY: 0.405 AC XY: 30112 AN XY: 74306

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.363

Alfa AF: 0.390 Hom.: 19961

Bravo AF: 0.387

Asia WGS AF: 0.337 AC: 1169 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	3.8
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7996797; hg19: chr13-47335990;