rs696116

Positions:

• chr1-74623555-A-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERICH3	NM_001002912.5	c.820-2641T>G		intron_variant		ENST00000326665.10
ERICH3-AS1	NR_121671.1	n.2331A>C		non_coding_transcript_exon_variant	3/3
ERICH3	XM_017000275.2	c.814-2641T>G		intron_variant
ERICH3-AS1	NR_121670.1	n.2424A>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERICH3	ENST00000326665.10	c.820-2641T>G		intron_variant		5	NM_001002912.5	P3
ERICH3	ENST00000420661.6	c.229-2641T>G		intron_variant		1		A2
ERICH3-AS1	ENST00000612390.4	n.2331A>C		non_coding_transcript_exon_variant	3/3	1
ERICH3	ENST00000479666.1	c.229-270T>G		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0202

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.00582

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0346 Hom.: 61

Bravo AF: 0.0612

Asia WGS AF: 0.0140 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs696116; hg19: chr1-75089239;