16-80451940-C-T

Position:

• chr16-80451940-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

DYNLRB2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+76702G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000565050.5	n.598+39277G>A		intron_variant		5
DYNLRB2-AS1	ENST00000568776.5	n.252+76702G>A		intron_variant		4
DYNLRB2-AS1	ENST00000568819.5	n.362+40630G>A		intron_variant		5

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

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.671

Alfa AF: 0.628 Hom.: 25226

Bravo AF: 0.645

Asia WGS AF: 0.812 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8053391; hg19: chr16-80485837;