6-83859205-A-G

Variant names:

• chr6-83859205-A-G
• rs2296412
• NM_001400774.1:c.-27-4970A>G

Variant summary

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

The NM_001400774.1(RIPPLY2-CYB5R4):​c.-27-4970A>G variant causes a intron 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 NM_001400774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 7 publications found

Genes affected

RIPPLY2-CYB5R4 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001400774.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPPLY2-CYB5R4	NM_001400774.1		c.-27-4970A>G		intron	N/A	NP_001387703.1
	RIPPLY2-CYB5R4	NR_174603.1		n.235-4970A>G		intron	N/A
	RIPPLY2-CYB5R4	NR_174604.1		n.297-4970A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.456 AC: 18916 AN: 41438

American (AMR) AF: 0.210 AC: 3211 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5158

South Asian (SAS) AF: 0.0570 AC: 275 AN: 4828

European-Finnish (FIN) AF: 0.0526 AC: 558 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0346 AC: 2350 AN: 68004

Other (OTH) AF: 0.140 AC: 297 AN: 2116

Alfa AF: 0.0786 Hom.: 6369

Bravo AF: 0.207

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.48
PhyloP100		-0.26
PromoterAI		0.00070	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2296412; hg19: chr6-84568924;