rs10514498

Positions:

• chr16-80440621-G-C
• chr16-80440621-G-T

Variant summary

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

The NR_120307.1(DYNLRB2-AS1):​n.252+88021C>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 0.125 in 152,170 control chromosomes in the GnomAD database, including 1,254 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 0.12 (1254 hom., cov: 33)
• Consequence: DYNLRB2-AS1 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+88021C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNLRB2-AS1	ENST00000668341.1	n.417+88021C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18943 AN: 152052 Hom.: 1252 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.125 AC: 18958 AN: 152170 Hom.: 1254 Cov.: 33 AF XY: 0.126 AC XY: 9384 AN XY: 74404

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0801

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0654 Hom.: 83

Bravo AF: 0.117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514498; hg19: chr16-80474518;