rs28129

chr5-96819815-G-A

Variant summary

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

The ENST00000501338.5(ENSG00000247121):n.1962+3122C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,062 control chromosomes in the GnomAD database, including 33,671 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 0.66 (33671 hom., cov: 32)
• Consequence: ENST00000501338.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERAP1	XM_011543484.3	c.-267+3122C>T		intron_variant
ERAP1	XM_011543485.3	c.-270-5505C>T		intron_variant
ERAP1	XM_011543486.4	c.-271+3122C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501338.5	n.1962+3122C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100350 AN: 151944 Hom.: 33646 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.660 AC: 100436 AN: 152062 Hom.: 33671 Cov.: 32 AF XY: 0.657 AC XY: 48826 AN XY: 74314

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.651

Alfa AF: 0.692 Hom.: 16739

Bravo AF: 0.649

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.5
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28129; hg19: chr5-96155518;