16-13915962-T-C

Variant names:

• chr16-13915962-T-C
• rs12926685
• XR_007064999.1:n.83-7234A>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.83-7234A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,892 control chromosomes in the GnomAD database, including 8,768 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 0.34 (8768 hom., cov: 33)
• Consequence: LOC105371093 XR_007064999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.338 AC: 51300 AN: 151774 Hom.: 8749 Cov.: 33

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.338 AC: 51365 AN: 151892 Hom.: 8768 Cov.: 33 AF XY: 0.334 AC XY: 24807 AN XY: 74220

African (AFR) AF: 0.317 AC: 13147 AN: 41430

American (AMR) AF: 0.333 AC: 5080 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1411 AN: 3462

East Asian (EAS) AF: 0.260 AC: 1343 AN: 5166

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4824

European-Finnish (FIN) AF: 0.317 AC: 3341 AN: 10550

Middle Eastern (MID) AF: 0.431 AC: 124 AN: 288

European-Non Finnish (NFE) AF: 0.356 AC: 24164 AN: 67904

Other (OTH) AF: 0.369 AC: 777 AN: 2106

Alfa AF: 0.355 Hom.: 12740

Bravo AF: 0.340

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.40
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs12926685; hg19: chr16-14009819;