rs289745

Variant names:

• chr16-56985620-C-A
• rs289745
• XR_007065081.1:n.3533G>T

Variant summary

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

The XR_007065081.1(LOC124903696):​n.3533G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,104 control chromosomes in the GnomAD database, including 32,253 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 0.65 (32253 hom., cov: 32)
• Consequence: LOC124903696 XR_007065081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 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: 0.645 AC: 98073 AN: 151986 Hom.: 32216 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.645 AC: 98161 AN: 152104 Hom.: 32253 Cov.: 32 AF XY: 0.644 AC XY: 47927 AN XY: 74370

African (AFR) AF: 0.766 AC: 31800 AN: 41502

American (AMR) AF: 0.586 AC: 8952 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1932 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2713 AN: 5164

South Asian (SAS) AF: 0.517 AC: 2494 AN: 4826

European-Finnish (FIN) AF: 0.657 AC: 6956 AN: 10586

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41274 AN: 67956

Other (OTH) AF: 0.634 AC: 1338 AN: 2112

Alfa AF: 0.616 Hom.: 87349

Bravo AF: 0.650

Asia WGS AF: 0.523 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.69
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs289745; hg19: chr16-57019532;