Variant chr1-44616668-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018150.4(RNF220):c.758+2371G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,680 control chromosomes in the GnomAD database, including 17,877 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 0.47 ( 17877 hom., cov: 30)

Consequence

RNF220
NM_018150.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.678

Variant links:

Genes affected

RNF220 (HGNC:25552): (ring finger protein 220) Predicted to enable ubiquitin protein ligase activity. Involved in positive regulation of canonical Wnt signaling pathway. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

RNF220 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNF220	NM_018150.4 linkuse as main transcript	c.758+2371G>A		intron_variant		ENST00000361799.7	NP_060620.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
RNF220	ENST00000361799.7 linkuse as main transcript	c.758+2371G>A	intron_variant	1	NM_018150.4	ENSP00000354872	P1	Q5VTB9-1
RNF220	ENST00000355387.6 linkuse as main transcript	c.758+2371G>A	intron_variant	1		ENSP00000347548	P1	Q5VTB9-1
RNF220	ENST00000496262.1 linkuse as main transcript	n.33+2371G>A	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.474

AC:

71895

AN:

151562

Hom.:

17875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.367

Gnomad AMI

AF:

0.452

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.562

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.567

Gnomad OTH

AF:

0.483

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

GnomAD4 genome

AF:

0.474

AC:

71920

AN:

151680

Hom.:

17877

Cov.:

AF XY:

0.468

AC XY:

34691

AN XY:

74112

show subpopulations

Gnomad4 AFR

AF:

0.367

Gnomad4 AMR

AF:

0.381

Gnomad4 ASJ

AF:

0.512

Gnomad4 EAS

AF:

0.230

Gnomad4 SAS

AF:

0.420

Gnomad4 FIN

AF:

0.562

Gnomad4 NFE

AF:

0.567

Gnomad4 OTH

AF:

0.478

Alfa

AF:

0.537

Hom.:

21517

Bravo

AF:

0.454

Asia WGS

AF:

0.301

AC:

1050

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.2

DANN

Benign

0.55

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over