XR_007064999.1:n.83-6833C>G

Variant names:

• chr16-13915561-G-C
• rs11649492
• XR_007064999.1:n.83-6833C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064999.1(LOC105371093):​n.83-6833C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,032 control chromosomes in the GnomAD database, including 8,477 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 (8477 hom., cov: 33)
• Consequence: LOC105371093 XR_007064999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 4 publications found

Genes affected

LOC105371093 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50392 AN: 151914 Hom.: 8461 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.332 AC: 50455 AN: 152032 Hom.: 8477 Cov.: 33 AF XY: 0.328 AC XY: 24372 AN XY: 74292

African (AFR) AF: 0.311 AC: 12912 AN: 41468

American (AMR) AF: 0.328 AC: 5015 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1369 AN: 5174

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4816

European-Finnish (FIN) AF: 0.314 AC: 3309 AN: 10546

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23602 AN: 67976

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.190 Hom.: 387

Bravo AF: 0.332

Asia WGS AF: 0.323 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.21
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11649492; hg19: chr16-14009418;