16-80451940-C-T

Variant names:

• chr16-80451940-C-T
• rs8053391
• ENST00000565050.5:n.598+39277G>A

Variant summary

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

The ENST00000568776.5(DYNLRB2-AS1):​n.252+76702G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,086 control chromosomes in the GnomAD database, including 32,474 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 (32474 hom., cov: 33)
• Consequence: DYNLRB2-AS1 ENST00000568776.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568776.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	NR_120307.1		n.252+76702G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	ENST00000565050.5	TSL:5	n.598+39277G>A		intron	N/A
	DYNLRB2-AS1	ENST00000568776.5	TSL:4	n.252+76702G>A		intron	N/A
	DYNLRB2-AS1	ENST00000568819.5	TSL:5	n.362+40630G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98728 AN: 151968 Hom.: 32442 Cov.: 33

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.650 AC: 98812 AN: 152086 Hom.: 32474 Cov.: 33 AF XY: 0.659 AC XY: 49009 AN XY: 74352

African (AFR) AF: 0.566 AC: 23486 AN: 41468

American (AMR) AF: 0.726 AC: 11097 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3472

East Asian (EAS) AF: 0.772 AC: 3998 AN: 5176

South Asian (SAS) AF: 0.845 AC: 4074 AN: 4824

European-Finnish (FIN) AF: 0.746 AC: 7890 AN: 10580

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43329 AN: 67972

Other (OTH) AF: 0.671 AC: 1413 AN: 2106

Alfa AF: 0.627 Hom.: 33906

Bravo AF: 0.645

Asia WGS AF: 0.812 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.51
PhyloP100		0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8053391;

hg19: chr16-80485837;