rs439825

Positions:

• chr15-22561372-G-A
• chr15-22561372-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_002824.3(HERC2P2):​n.3412G>A variant causes a non coding transcript exon change. 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 0.00011 (0 hom., cov: 21)
  • Exomes 𝑓: 0.000068 (36 hom.)
  • Failed GnomAD Quality Control
• Consequence: HERC2P2 NR_002824.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.80

Genes affected

HERC2P2 (HGNC:4870): (HERC2 pseudogene 2)

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HERC2P2	NR_002824.3	n.3412G>A		non_coding_transcript_exon_variant	22/35

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HERC2P2	ENST00000613386.4	n.3293G>A		non_coding_transcript_exon_variant	21/32
	ENST00000619021.4	n.3157G>A		non_coding_transcript_exon_variant	20/32	1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 16 AN: 131250 Hom.: 0 Cov.: 21 FAILED QC

Gnomad AFR AF: 0.0000924

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000757

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000204

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.000579

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000682 AC: 91 AN: 1334258 Hom.: 36 Cov.: 28 AF XY: 0.0000872 AC XY: 58 AN XY: 665134

Gnomad4 AFR exome AF: 0.000210

Gnomad4 AMR exome AF: 0.000309

Gnomad4 ASJ exome AF: 0.0000432

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000338

Gnomad4 FIN exome AF: 0.0000387

Gnomad4 NFE exome AF: 0.0000315

Gnomad4 OTH exome AF: 0.000164

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000114 AC: 15 AN: 131342 Hom.: 0 Cov.: 21 AF XY: 0.0000939 AC XY: 6 AN XY: 63876

Gnomad4 AFR AF: 0.0000921

Gnomad4 AMR AF: 0.0000756

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000103

Gnomad4 NFE AF: 0.000147

Gnomad4 OTH AF: 0.000572

Alfa AF: 0.00101 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	16
DANN	Benign	0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs439825; hg19: chr15-23311724;