rs7183877

chr15-28120587-C-A

Variant summary

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

The NM_004667.6(HERC2):c.13272+759G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,198 control chromosomes in the GnomAD database, including 1,196 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 0.11 (1196 hom., cov: 33)
• Consequence: HERC2 NM_004667.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

Genes affected

HERC2 (HGNC:4868): (HECT and RLD domain containing E3 ubiquitin protein ligase 2) This gene belongs to the HERC gene family that encodes a group of unusually large proteins, which contain multiple structural domains. All members have at least 1 copy of an N-terminal region showing homology to the cell cycle regulator RCC1 and a C-terminal HECT (homologous to E6-AP C terminus) domain found in a number of E3 ubiquitin protein ligases. Genetic variations in this gene are associated with skin/hair/eye pigmentation variability. Multiple pseudogenes of this gene are located on chromosomes 15 and 16. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HERC2	NM_004667.6	c.13272+759G>T		intron_variant		ENST00000261609.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HERC2	ENST00000261609.13	c.13272+759G>T		intron_variant		1	NM_004667.6	P1
HERC2	ENST00000650509.1	c.*386+759G>T		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16207 AN: 152080 Hom.: 1190 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0178

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.107 AC: 16221 AN: 152198 Hom.: 1196 Cov.: 33 AF XY: 0.110 AC XY: 8149 AN XY: 74414

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.0178

Gnomad4 NFE AF: 0.0752

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0970 Hom.: 1254

Bravo AF: 0.122

Asia WGS AF: 0.209 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.7
Dann	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7183877; hg19: chr15-28365733;