rs2296412

Positions:

• chr6-83859205-A-G

Variant summary

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

The NR_174604.1(RIPPLY2-CYB5R4):​n.297-4970A>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 0.178 in 152,110 control chromosomes in the GnomAD database, including 5,026 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 0.18 (5026 hom., cov: 32)
• Consequence: RIPPLY2-CYB5R4 NR_174604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

RIPPLY2-CYB5R4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIPPLY2-CYB5R4	NR_174604.1	n.297-4970A>G		intron_variant, non_coding_transcript_variant
RIPPLY2-CYB5R4	NM_001400774.1	c.-27-4970A>G		intron_variant
RIPPLY2-CYB5R4	NR_174603.1	n.235-4970A>G		intron_variant, non_coding_transcript_variant
RIPPLY2-CYB5R4	NR_174605.1	n.456-4970A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27004 AN: 151992 Hom.: 5007 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.178 AC: 27082 AN: 152110 Hom.: 5026 Cov.: 32 AF XY: 0.177 AC XY: 13181 AN XY: 74366

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0567 Hom.: 1522

Bravo AF: 0.207

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296412; hg19: chr6-84568924;