rs2626640

Positions:

• chr16-80335372-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120307.1(DYNLRB2-AS1):​n.253-175066A>G variant causes a intron, non coding transcript 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 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.253-175066A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000668341.1	n.418-175051A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.336

Alfa AF: 0.275 Hom.: 10276

Bravo AF: 0.369

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2626640; hg19: chr16-80369269;