rs9931491

Variant names:

• chr16-80227771-C-G
• rs9931491
• ENST00000565050.5:n.599-68316G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000565050.5(DYNLRB2-AS1):​n.599-68316G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 152,076 control chromosomes in the GnomAD database, including 30 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 0.012 (30 hom., cov: 32)
• Consequence: DYNLRB2-AS1 ENST00000565050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 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=-0.97).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0115 (1755/152076) while in subpopulation AFR AF = 0.0403 (1670/41470). AF 95% confidence interval is 0.0387. There are 30 homozygotes in GnomAd4. There are 825 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 30 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565050.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	NR_120307.1		n.253-67465G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	ENST00000565050.5	TSL:5	n.599-68316G>C		intron	N/A
	DYNLRB2-AS1	ENST00000568776.5	TSL:4	n.253-67465G>C		intron	N/A
	DYNLRB2-AS1	ENST00000568819.5	TSL:5	n.363-8905G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0115 AC: 1755 AN: 151958 Hom.: 30 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00321

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000279

Gnomad OTH AF: 0.00766

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

GnomAD4 genome AF: 0.0115 AC: 1755 AN: 152076 Hom.: 30 Cov.: 32 AF XY: 0.0111 AC XY: 825 AN XY: 74324

African (AFR) AF: 0.0403 AC: 1670 AN: 41470

American (AMR) AF: 0.00321 AC: 49 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00 AC: 0 AN: 4794

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10578

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000279 AC: 19 AN: 68002

Other (OTH) AF: 0.00758 AC: 16 AN: 2110

Alfa AF: 0.00915 Hom.: 0

Bravo AF: 0.0134

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9931491; hg19: chr16-80261668;