chr13-46761855-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

LOC107984563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.411 AC: 17046 AN: 41444

American (AMR) AF: 0.372 AC: 5688 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1048 AN: 3462

East Asian (EAS) AF: 0.291 AC: 1505 AN: 5180

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4818

European-Finnish (FIN) AF: 0.511 AC: 5397 AN: 10562

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26874 AN: 67970

Other (OTH) AF: 0.363 AC: 767 AN: 2112

Alfa AF: 0.392 Hom.: 46341

Bravo AF: 0.387

Asia WGS AF: 0.337 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.35
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7996797; hg19: chr13-47335990;