chr16-55652906-T-A

Variant names:

• chr16-55652906-T-A
• rs28386840
• XR_007065075.1:n.*200A>T

Variant summary

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

The XR_007065075.1(LOC124903693):​n.*200A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 145,034 control chromosomes in the GnomAD database, including 29,748 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 0.64 (29748 hom., cov: 32)
• Consequence: LOC124903693 XR_007065075.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 50 publications found

Genes affected

LOC124903693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 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: 0.639 AC: 92600 AN: 144926 Hom.: 29725 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.639 AC: 92666 AN: 145034 Hom.: 29748 Cov.: 32 AF XY: 0.644 AC XY: 45735 AN XY: 70978

African (AFR) AF: 0.455 AC: 16248 AN: 35728

American (AMR) AF: 0.694 AC: 10456 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2258 AN: 3378

East Asian (EAS) AF: 0.559 AC: 2881 AN: 5156

South Asian (SAS) AF: 0.712 AC: 3414 AN: 4792

European-Finnish (FIN) AF: 0.735 AC: 7767 AN: 10564

Middle Eastern (MID) AF: 0.588 AC: 167 AN: 284

European-Non Finnish (NFE) AF: 0.709 AC: 47554 AN: 67106

Other (OTH) AF: 0.644 AC: 1319 AN: 2048

Alfa AF: 0.367 Hom.: 530

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs28386840; hg19: chr16-55686818;