5-96824289-A-C

Position:

• chr5-96824289-A-C

Variant summary

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

The ENST00000501338.5(ENSG00000247121):​n.1782-1172T>G 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 0.897 in 152,200 control chromosomes in the GnomAD database, including 61,794 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 0.90 (61794 hom., cov: 30)
• Consequence: ENST00000501338.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERAP1	XM_011543484.3	c.-450-1169T>G		intron_variant
ERAP1	XM_011543485.3	c.-270-9979T>G		intron_variant
ERAP1	XM_011543486.4	c.-454-1169T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501338.5	n.1782-1172T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136440 AN: 152082 Hom.: 61734 Cov.: 30

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.897 AC: 136562 AN: 152200 Hom.: 61794 Cov.: 30 AF XY: 0.893 AC XY: 66465 AN XY: 74414

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.891

Alfa AF: 0.915 Hom.: 40795

Bravo AF: 0.891

Asia WGS AF: 0.746 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs151823; hg19: chr5-96159992;