16-56984190-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903696	XR_007065081.1	n.*52C>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;