rs17666538

Variant names:

• chr8-616207-T-C
• rs17666538
• ENST00000523415.5:n.*1799A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523415.5(ERICH1):​n.*1799A>G variant causes a non coding transcript exon 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 ENST00000523415.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 9 publications found

Genes affected

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

LOC124902055 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523415.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH1	NM_001303100.2		c.*364A>G		3_prime_UTR	Exon 6 of 6	NP_001290029.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH1	ENST00000523415.5	TSL:2	n.*1799A>G		non_coding_transcript_exon	Exon 4 of 4	ENSP00000430296.1
	ERICH1	ENST00000523415.5	TSL:2	n.*1799A>G		3_prime_UTR	Exon 4 of 4	ENSP00000430296.1
	ERICH1	ENST00000522706.5	TSL:5	c.977-923A>G		intron	N/A	ENSP00000428635.1

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

African (AFR) AF: 0.0110 AC: 18 AN: 1630

American (AMR) AF: 0.100 AC: 389 AN: 3890

Ashkenazi Jewish (ASJ) AF: 0.0537 AC: 76 AN: 1414

East Asian (EAS) AF: 0.0516 AC: 129 AN: 2502

South Asian (SAS) AF: 0.0446 AC: 517 AN: 11594

European-Finnish (FIN) AF: 0.139 AC: 422 AN: 3028

Middle Eastern (MID) AF: 0.0320 AC: 8 AN: 250

European-Non Finnish (NFE) AF: 0.0862 AC: 3491 AN: 40516

Other (OTH) AF: 0.0748 AC: 282 AN: 3772

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

African (AFR) AF: 0.0148 AC: 616 AN: 41564

American (AMR) AF: 0.0743 AC: 1137 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3468

East Asian (EAS) AF: 0.0648 AC: 336 AN: 5182

South Asian (SAS) AF: 0.0371 AC: 179 AN: 4828

European-Finnish (FIN) AF: 0.132 AC: 1399 AN: 10594

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5235 AN: 68024

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0660 Hom.: 876

Bravo AF: 0.0545

Asia WGS AF: 0.0490 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.54
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17666538; hg19: chr8-566207;