rs62376445

Positions:

• chr5-96861018-C-A
• chr5-96861018-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000501338.5(ENSG00000247121):​n.1781+12268G>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 0.0257 in 151,710 control chromosomes in the GnomAD database, including 87 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 0.026 (87 hom., cov: 32)
• Consequence: ENST00000501338.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0257 (3898/151710) while in subpopulation NFE AF= 0.0421 (2861/67950). AF 95% confidence interval is 0.0408. There are 87 homozygotes in gnomad4. There are 1741 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 87 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERAP1	XM_011543484.3	c.-451+12268G>T		intron_variant
ERAP1	XM_011543485.3	c.-271+12268G>T		intron_variant
ERAP1	XM_011543486.4	c.-455+12268G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501338.5	n.1781+12268G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3899 AN: 151594 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.00665

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0176

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0257 AC: 3898 AN: 151710 Hom.: 87 Cov.: 32 AF XY: 0.0235 AC XY: 1741 AN XY: 74102

Gnomad4 AFR AF: 0.00663

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0204

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0421

Gnomad4 OTH AF: 0.0299

Alfa AF: 0.00987 Hom.: 9

Bravo AF: 0.0264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62376445; hg19: chr5-96196721;