rs845028

Positions:

• chr5-96834519-G-A

Variant summary

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

The ENST00000501338.5(ENSG00000247121):​n.1782-11402C>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 0.71 in 152,102 control chromosomes in the GnomAD database, including 39,328 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 0.71 (39328 hom., cov: 32)
• Consequence: ENST00000501338.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERAP1	XM_011543484.3	c.-450-11399C>T		intron_variant
ERAP1	XM_011543485.3	c.-270-20209C>T		intron_variant
ERAP1	XM_011543486.4	c.-454-11399C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501338.5	n.1782-11402C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107922 AN: 151984 Hom.: 39305 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.710 AC: 108007 AN: 152102 Hom.: 39328 Cov.: 32 AF XY: 0.711 AC XY: 52876 AN XY: 74340

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.722

Alfa AF: 0.760 Hom.: 17103

Bravo AF: 0.693

Asia WGS AF: 0.670 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.092
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs845028; hg19: chr5-96170222;