rs1125733

Variant names:

• chr16-80418343-A-G
• rs1125733
• ENST00000565050.5:n.598+72874T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000565050.5(DYNLRB2-AS1):​n.598+72874T>C variant causes a intron change. The variant allele was found at a frequency of 0.332 in 149,034 control chromosomes in the GnomAD database, including 9,800 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 0.33 (9800 hom., cov: 32)
• Consequence: DYNLRB2-AS1 ENST00000565050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.64
• Publications: 3 publications found

Genes affected

DYNLRB2-AS1 (HGNC:55405): (DYNLRB2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+110299T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000565050.5	n.598+72874T>C		intron_variant	Intron 3 of 4	5
DYNLRB2-AS1	ENST00000568776.5	n.252+110299T>C		intron_variant	Intron 2 of 5	4
DYNLRB2-AS1	ENST00000568819.5	n.362+74227T>C		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.332 AC: 49513 AN: 148914 Hom.: 9804 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.441

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.332 AC: 49512 AN: 149034 Hom.: 9800 Cov.: 32 AF XY: 0.330 AC XY: 24070 AN XY: 72888

African (AFR) AF: 0.106 AC: 4375 AN: 41164

American (AMR) AF: 0.298 AC: 4497 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1163 AN: 3382

East Asian (EAS) AF: 0.374 AC: 1932 AN: 5164

South Asian (SAS) AF: 0.249 AC: 1193 AN: 4788

European-Finnish (FIN) AF: 0.416 AC: 4294 AN: 10310

Middle Eastern (MID) AF: 0.429 AC: 121 AN: 282

European-Non Finnish (NFE) AF: 0.466 AC: 30695 AN: 65894

Other (OTH) AF: 0.360 AC: 747 AN: 2074

Alfa AF: 0.410 Hom.: 16984

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	18
DANN	Benign	0.84
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs1125733; hg19: chr16-80452240;