rs439825

Variant names:

• chr15-22561372-G-A
• rs439825
• ENST00000619021.5:n.3523G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000619021.5(ENSG00000291003):​n.3523G>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: ENSG00000291003 ENST00000619021.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.80
• Publications: 1 publications found

Genes affected

ENSG00000291003 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HERC2P2	NR_002824.3	n.3412G>A		non_coding_transcript_exon_variant	Exon 22 of 35

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291003	ENST00000619021.5	n.3523G>A		non_coding_transcript_exon_variant	Exon 23 of 35	1
HERC2P2	ENST00000613386.4	n.3293G>A		non_coding_transcript_exon_variant	Exon 21 of 32	6
ENSG00000291003	ENST00000835776.1	n.1090G>A		non_coding_transcript_exon_variant	Exon 4 of 6

Frequencies

GnomAD3 genomes AF: 0.000122 AC: 16 AN: 131250 Hom.: 0 Cov.: 21

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

African (AFR) AF: 0.000210 AC: 6 AN: 28544

American (AMR) AF: 0.000309 AC: 13 AN: 42090

Ashkenazi Jewish (ASJ) AF: 0.0000432 AC: 1 AN: 23172

East Asian (EAS) AF: 0.00 AC: 0 AN: 39308

South Asian (SAS) AF: 0.000338 AC: 26 AN: 76836

European-Finnish (FIN) AF: 0.0000387 AC: 2 AN: 51688

Middle Eastern (MID) AF: 0.000574 AC: 2 AN: 3482

European-Non Finnish (NFE) AF: 0.0000315 AC: 32 AN: 1014292

Other (OTH) AF: 0.000164 AC: 9 AN: 54846

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000921 AC: 3 AN: 32570

American (AMR) AF: 0.0000756 AC: 1 AN: 13224

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2928

East Asian (EAS) AF: 0.00 AC: 0 AN: 4880

South Asian (SAS) AF: 0.00 AC: 0 AN: 3806

European-Finnish (FIN) AF: 0.000103 AC: 1 AN: 9722

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 232

European-Non Finnish (NFE) AF: 0.000147 AC: 9 AN: 61424

Other (OTH) AF: 0.000572 AC: 1 AN: 1748

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		6.8
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

Other links and lift over

dbSNP: rs439825; hg19: chr15-23311724;