rs696116

Variant names:

• chr1-74623555-A-C
• rs696116
• NM_001002912.5:c.820-2641T>G

Variant summary

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

The NM_001002912.5(ERICH3):​c.820-2641T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 152,188 control chromosomes in the GnomAD database, including 672 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 0.054 (672 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ERICH3 NM_001002912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

Genes affected

ERICH3 (HGNC:25346): (glutamate rich 3)

ERICH3-AS1 (HGNC:41093): (ERICH3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002912.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH3	NM_001002912.5	MANE Select	c.820-2641T>G		intron	N/A	NP_001002912.4
	ERICH3-AS1	NR_121670.1		n.2424A>C		non_coding_transcript_exon	Exon 3 of 3
	ERICH3-AS1	NR_121671.1		n.2331A>C		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH3	ENST00000326665.10	TSL:5 MANE Select	c.820-2641T>G		intron	N/A	ENSP00000322609.5
	ERICH3	ENST00000420661.6	TSL:1	c.229-2641T>G		intron	N/A	ENSP00000398581.2
	ERICH3-AS1	ENST00000612390.4	TSL:1	n.2331A>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8196 AN: 152070 Hom.: 672 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00582

Gnomad OTH AF: 0.0459

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 10

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0540 AC: 8219 AN: 152188 Hom.: 672 Cov.: 32 AF XY: 0.0527 AC XY: 3921 AN XY: 74430

African (AFR) AF: 0.174 AC: 7223 AN: 41486

American (AMR) AF: 0.0202 AC: 309 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5160

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4826

European-Finnish (FIN) AF: 0.0105 AC: 112 AN: 10626

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00582 AC: 396 AN: 68020

Other (OTH) AF: 0.0459 AC: 97 AN: 2112

Alfa AF: 0.0404 Hom.: 80

Bravo AF: 0.0612

Asia WGS AF: 0.0140 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.64
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs696116; hg19: chr1-75089239;