rs1570023

Variant names:

• chr20-62411193-T-C
• rs1570023
• NM_080833.3:c.1877-197A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RBBP8NL	NM_080833.3	c.1877-197A>G		intron_variant	Intron 13 of 13	ENST00000252998.2	NP_543023.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBBP8NL	ENST00000252998.2	c.1877-197A>G		intron_variant	Intron 13 of 13	2	NM_080833.3	ENSP00000252998.1

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

African (AFR) AF: 0.172 AC: 7131 AN: 41506

American (AMR) AF: 0.139 AC: 2131 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0677 AC: 326 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11843 AN: 67958

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.173 Hom.: 4210

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
PhyloP100		-3.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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