rs1325471

chr6-83857956-A-Gchr6-83857956-A-T

Variant summary

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

The NR_174604.1(RIPPLY2-CYB5R4):n.296+3795A>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 0.283 in 152,104 control chromosomes in the GnomAD database, including 11,907 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 0.28 (11907 hom., cov: 33)
• Consequence: RIPPLY2-CYB5R4 NR_174604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

Genes affected

RIPPLY2-CYB5R4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIPPLY2-CYB5R4	NR_174604.1	n.296+3795A>G		intron_variant, non_coding_transcript_variant
RIPPLY2-CYB5R4	NM_001400774.1	c.-28+3795A>G		intron_variant
RIPPLY2-CYB5R4	NR_174603.1	n.234+3795A>G		intron_variant, non_coding_transcript_variant
RIPPLY2-CYB5R4	NR_174605.1	n.455+3897A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42964 AN: 151984 Hom.: 11865 Cov.: 33

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0813

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.283 AC: 43074 AN: 152104 Hom.: 11907 Cov.: 33 AF XY: 0.281 AC XY: 20877 AN XY: 74378

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.0782

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.0711

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0812

Gnomad4 OTH AF: 0.233

Alfa AF: 0.193 Hom.: 1145

Bravo AF: 0.317

Asia WGS AF: 0.183 AC: 638 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.0
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325471; hg19: chr6-84567675;