rs17666538

Positions:

• chr8-616207-T-C

Variant summary

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

The NM_001303100.2(ERICH1):​c.*364A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 220,870 control chromosomes in the GnomAD database, including 661 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 0.060 (388 hom., cov: 33)
  • Exomes 𝑓: 0.078 (273 hom.)
• Consequence: ERICH1 NM_001303100.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592

Genes affected

ERICH1 (HGNC:27234): (glutamate rich 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERICH1	NM_001303100.2	c.*364A>G		3_prime_UTR_variant	6/6		NP_001290029.1
ERICH1	XM_047421399.1	c.1442-923A>G		intron_variant			XP_047277355.1
ERICH1	XM_047421403.1	c.1259-923A>G		intron_variant			XP_047277359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERICH1	ENST00000522706.5	c.977-923A>G		intron_variant		5		ENSP00000428635	A2
ERICH1	ENST00000523415.5	c.*1799A>G		3_prime_UTR_variant, NMD_transcript_variant	4/4	2		ENSP00000430296

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9171 AN: 152156 Hom.: 389 Cov.: 33

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0651

Gnomad SAS AF: 0.0370

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.0445

GnomAD4 exome AF: 0.0777 AC: 5332 AN: 68596 Hom.: 273 Cov.: 0 AF XY: 0.0723 AC XY: 2622 AN XY: 36246

Gnomad4 AFR exome AF: 0.0110

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.0537

Gnomad4 EAS exome AF: 0.0516

Gnomad4 SAS exome AF: 0.0446

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.0862

Gnomad4 OTH exome AF: 0.0748

GnomAD4 genome AF: 0.0602 AC: 9168 AN: 152274 Hom.: 388 Cov.: 33 AF XY: 0.0625 AC XY: 4651 AN XY: 74438

Gnomad4 AFR AF: 0.0148

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0648

Gnomad4 SAS AF: 0.0371

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0770

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0708 Hom.: 614

Bravo AF: 0.0545

Asia WGS AF: 0.0490 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17666538; hg19: chr8-566207;