rs1981846

Positions:

• chr5-96933158-C-A
• chr5-96933158-C-T

Variant summary

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

The ENST00000501338.5(ENSG00000247121):​n.1688+964G>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 0.497 in 150,100 control chromosomes in the GnomAD database, including 18,728 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 0.50 (18728 hom., cov: 28)
• Consequence: ENST00000501338.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERAP1	XM_011543484.3	c.-702+964G>T		intron_variant			XP_011541786.1
ERAP1	XM_011543485.3	c.-522+964G>T		intron_variant			XP_011541787.1
ERAP1	XM_011543486.4	c.-706+964G>T		intron_variant			XP_011541788.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000501338.5	n.1688+964G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.497 AC: 74539 AN: 149996 Hom.: 18685 Cov.: 28

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.497 AC: 74643 AN: 150100 Hom.: 18728 Cov.: 28 AF XY: 0.494 AC XY: 36126 AN XY: 73122

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.488

Alfa AF: 0.479 Hom.: 8093

Bravo AF: 0.494

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981846; hg19: chr5-96268862;