chr1-74641057-G-A

Position:

• chr1-74641057-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERICH3	NM_001002912.5	c.444+274C>T		intron_variant		ENST00000326665.10
ERICH3	XM_017000275.2	c.438+274C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERICH3	ENST00000326665.10	c.444+274C>T		intron_variant		5	NM_001002912.5	P3

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

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.151

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs17095690; hg19: chr1-75106741;