rs17095690

Variant names:

• chr1-74641057-G-A
• rs17095690
• NM_001002912.5:c.444+274C>T

Variant summary

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

The NM_001002912.5(ERICH3):​c.444+274C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,924 control chromosomes in the GnomAD database, including 1,643 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 0.14 (1643 hom., cov: 32)
• Consequence: ERICH3 NM_001002912.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH3	NM_001002912.5	MANE Select	c.444+274C>T		intron	N/A	NP_001002912.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH3	ENST00000326665.10	TSL:5 MANE Select	c.444+274C>T		intron	N/A	ENSP00000322609.5

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20735 AN: 151806 Hom.: 1636 Cov.: 32

Gnomad AFR AF: 0.0795

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.137 AC: 20765 AN: 151924 Hom.: 1643 Cov.: 32 AF XY: 0.144 AC XY: 10684 AN XY: 74242

African (AFR) AF: 0.0797 AC: 3303 AN: 41454

American (AMR) AF: 0.171 AC: 2609 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3466

East Asian (EAS) AF: 0.255 AC: 1315 AN: 5148

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4822

European-Finnish (FIN) AF: 0.168 AC: 1774 AN: 10544

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9221 AN: 67948

Other (OTH) AF: 0.151 AC: 319 AN: 2110

Alfa AF: 0.144 Hom.: 261

Bravo AF: 0.130

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.69
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs17095690; hg19: chr1-75106741; COSMIC: COSV107367982;