chr16-56984190-G-T

Variant names:

• chr16-56984190-G-T
• rs289744
• XR_007065081.1:n.*52C>A

Variant summary

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

The XR_007065081.1(LOC124903696):​n.*52C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,918 control chromosomes in the GnomAD database, including 29,892 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 0.61 (29892 hom., cov: 32)
• Consequence: LOC124903696 XR_007065081.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 16 publications found

Genes affected

LOC124903696 (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 (AMR) allele frequency at 95% confidence interval = 0.693 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: 0.613 AC: 93057 AN: 151798 Hom.: 29869 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.613 AC: 93124 AN: 151918 Hom.: 29892 Cov.: 32 AF XY: 0.613 AC XY: 45507 AN XY: 74264

African (AFR) AF: 0.421 AC: 17449 AN: 41416

American (AMR) AF: 0.703 AC: 10742 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2067 AN: 3468

East Asian (EAS) AF: 0.686 AC: 3544 AN: 5164

South Asian (SAS) AF: 0.608 AC: 2922 AN: 4808

European-Finnish (FIN) AF: 0.658 AC: 6938 AN: 10542

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47412 AN: 67934

Other (OTH) AF: 0.651 AC: 1369 AN: 2104

Alfa AF: 0.673 Hom.: 21513

Bravo AF: 0.607

Asia WGS AF: 0.618 AC: 2152 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	0.0090
DANN	Benign	0.86
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs289744; hg19: chr16-57018102;