rs2296412

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-83859205-A-C
• chr6-83859205-A-G
• chr6-83859205-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001400774.1(RIPPLY2-CYB5R4):​c.-27-4970A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: RIPPLY2-CYB5R4 NM_001400774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 0 publications found

Genes affected

RIPPLY2-CYB5R4 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIPPLY2-CYB5R4	NM_001400774.1	c.-27-4970A>C		intron_variant	Intron 2 of 16		NP_001387703.1
RIPPLY2-CYB5R4	NR_174603.1	n.235-4970A>C		intron_variant	Intron 2 of 17
RIPPLY2-CYB5R4	NR_174604.1	n.297-4970A>C		intron_variant	Intron 3 of 17
RIPPLY2-CYB5R4	NR_174605.1	n.456-4970A>C		intron_variant	Intron 1 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.41
PhyloP100		-0.26
PromoterAI		0.051	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;