16-13911894-T-C

Variant names:

• chr16-13911894-T-C
• rs4781560
• XR_007064999.1:n.83-3166A>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.83-3166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,896 control chromosomes in the GnomAD database, including 12,635 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 0.37 (12635 hom., cov: 31)
• Consequence: LOC105371093 XR_007064999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 9 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.372 AC: 56491 AN: 151778 Hom.: 12597 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.373 AC: 56594 AN: 151896 Hom.: 12635 Cov.: 31 AF XY: 0.367 AC XY: 27229 AN XY: 74210

African (AFR) AF: 0.638 AC: 26381 AN: 41366

American (AMR) AF: 0.295 AC: 4501 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3468

East Asian (EAS) AF: 0.265 AC: 1370 AN: 5168

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4816

European-Finnish (FIN) AF: 0.266 AC: 2805 AN: 10530

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17964 AN: 67962

Other (OTH) AF: 0.347 AC: 731 AN: 2106

Alfa AF: 0.306 Hom.: 11415

Bravo AF: 0.387

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs4781560; hg19: chr16-14005751;