rs1570023

chr20-62411193-T-C

Variant summary

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

The NM_080833.3(RBBP8NL):c.1877-197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,144 control chromosomes in the GnomAD database, including 2,019 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 0.16 (2019 hom., cov: 34)
• Consequence: RBBP8NL NM_080833.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.46

Genes affected

RBBP8NL (HGNC:16144): (RBBP8 N-terminal like) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBBP8NL	NM_080833.3	c.1877-197A>G		intron_variant		ENST00000252998.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBBP8NL	ENST00000252998.2	c.1877-197A>G		intron_variant		2	NM_080833.3	P1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23919 AN: 152026 Hom.: 2006 Cov.: 34

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.158 AC: 23964 AN: 152144 Hom.: 2019 Cov.: 34 AF XY: 0.152 AC XY: 11328 AN XY: 74388

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0677

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.168

Alfa AF: 0.177 Hom.: 3188

Bravo AF: 0.162

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.54
Dann	Benign	0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1570023; hg19: chr20-60986249; COSMIC: COSV53351581; COSMIC: COSV53351581;