chr16-80335372-T-C

Variant names:

• chr16-80335372-T-C
• rs2626640
• ENST00000565050.5:n.598+155845A>G

Variant summary

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

The ENST00000568776.5(DYNLRB2-AS1):​n.253-175066A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,996 control chromosomes in the GnomAD database, including 10,461 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 0.35 (10461 hom., cov: 32)
• Consequence: DYNLRB2-AS1 ENST00000568776.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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.253-175066A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	ENST00000565050.5	TSL:5	n.598+155845A>G		intron	N/A
	DYNLRB2-AS1	ENST00000568776.5	TSL:4	n.253-175066A>G		intron	N/A
	DYNLRB2-AS1	ENST00000568819.5	TSL:5	n.363-116506A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53036 AN: 151878 Hom.: 10438 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.349 AC: 53113 AN: 151996 Hom.: 10461 Cov.: 32 AF XY: 0.351 AC XY: 26072 AN XY: 74290

African (AFR) AF: 0.525 AC: 21736 AN: 41432

American (AMR) AF: 0.416 AC: 6348 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3472

East Asian (EAS) AF: 0.240 AC: 1235 AN: 5156

South Asian (SAS) AF: 0.378 AC: 1826 AN: 4826

European-Finnish (FIN) AF: 0.239 AC: 2523 AN: 10560

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17218 AN: 67978

Other (OTH) AF: 0.336 AC: 707 AN: 2102

Alfa AF: 0.296 Hom.: 20084

Bravo AF: 0.369

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.29
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs2626640; hg19: chr16-80369269;