5-96826239-T-G

Position:

• chr5-96826239-T-G

Variant summary

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

The ENST00000501338.5(ENSG00000247121):​n.1782-3122A>C 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 0.726 in 152,146 control chromosomes in the GnomAD database, including 40,660 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 0.73 (40660 hom., cov: 33)
• Consequence: ENST00000501338.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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 = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERAP1	XM_011543484.3	c.-450-3119A>C		intron_variant			XP_011541786.1
ERAP1	XM_011543485.3	c.-270-11929A>C		intron_variant			XP_011541787.1
ERAP1	XM_011543486.4	c.-454-3119A>C		intron_variant			XP_011541788.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000501338.5	n.1782-3122A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110310 AN: 152028 Hom.: 40619 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.726 AC: 110413 AN: 152146 Hom.: 40660 Cov.: 33 AF XY: 0.723 AC XY: 53763 AN XY: 74372

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.710

Alfa AF: 0.764 Hom.: 17311

Bravo AF: 0.714

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.012
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs152280; hg19: chr5-96161942;