15-22561372-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000619021.5(ENSG00000291003):​n.3523G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.00000682 in 1,465,690 control chromosomes in the GnomAD database, including 3 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 0.0000076 (0 hom., cov: 21)
  • Exomes 𝑓: 0.0000067 (3 hom.)
• 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: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BS2: High Homozygotes in GnomAdExome4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619021.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HERC2P2	NR_002824.3		n.3412G>T		non_coding_transcript_exon	Exon 22 of 35

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291003	ENST00000619021.5	TSL:1	n.3523G>T		non_coding_transcript_exon	Exon 23 of 35
	HERC2P2	ENST00000613386.4	TSL:6	n.3293G>T		non_coding_transcript_exon	Exon 21 of 32
	ENSG00000291003	ENST00000835776.1		n.1090G>T		non_coding_transcript_exon	Exon 4 of 6

Frequencies

GnomAD3 genomes AF: 0.00000761 AC: 1 AN: 131372 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000163

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000675 AC: 9 AN: 1334318 Hom.: 3 Cov.: 28 AF XY: 0.00000902 AC XY: 6 AN XY: 665166

African (AFR) AF: 0.00 AC: 0 AN: 28560

American (AMR) AF: 0.00 AC: 0 AN: 42092

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23172

East Asian (EAS) AF: 0.00 AC: 0 AN: 39310

South Asian (SAS) AF: 0.00 AC: 0 AN: 76842

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51690

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3482

European-Non Finnish (NFE) AF: 0.00000887 AC: 9 AN: 1014320

Other (OTH) AF: 0.00 AC: 0 AN: 54850

GnomAD4 genome AF: 0.00000761 AC: 1 AN: 131372 Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0 AN XY: 63860

African (AFR) AF: 0.00 AC: 0 AN: 32526

American (AMR) AF: 0.00 AC: 0 AN: 13218

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2930

East Asian (EAS) AF: 0.00 AC: 0 AN: 4896

South Asian (SAS) AF: 0.00 AC: 0 AN: 3816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9730

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 244

European-Non Finnish (NFE) AF: 0.0000163 AC: 1 AN: 61472

Other (OTH) AF: 0.00 AC: 0 AN: 1732

Alfa AF: 0.00 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.70
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;