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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903696	XR_007065081.1	n.3533G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

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

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 v4.3

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;