rs10514498

Variant names:

• chr16-80440621-G-C
• rs10514498
• ENST00000565050.5:n.598+50596C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000565050.5(DYNLRB2-AS1):​n.598+50596C>G variant causes a intron 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 ENST00000565050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• 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=-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 rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+88021C>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000565050.5	n.598+50596C>G		intron_variant	Intron 3 of 4	5
DYNLRB2-AS1	ENST00000568776.5	n.252+88021C>G		intron_variant	Intron 2 of 5	4
DYNLRB2-AS1	ENST00000568819.5	n.362+51949C>G		intron_variant	Intron 3 of 4	5

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

African (AFR) AF: 0.150 AC: 6238 AN: 41518

American (AMR) AF: 0.0801 AC: 1225 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3472

East Asian (EAS) AF: 0.135 AC: 698 AN: 5186

South Asian (SAS) AF: 0.172 AC: 828 AN: 4818

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10598

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7630 AN: 67972

Other (OTH) AF: 0.112 AC: 237 AN: 2110

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10514498; hg19: chr16-80474518;