8-642876-C-T

Position:

• chr8-642876-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001303100.2(ERICH1):​c.1258+25722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,918 control chromosomes in the GnomAD database, including 19,497 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 0.50 (19497 hom., cov: 31)
• Consequence: ERICH1 NM_001303100.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

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

ERICH1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERICH1	NM_001303100.2	c.1258+25722G>A		intron_variant			NP_001290029.1
ERICH1	XM_047421393.1	c.1442-2042G>A		intron_variant			XP_047277349.1
ERICH1	XM_006716234.5	c.1259-2042G>A		intron_variant			XP_006716297.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERICH1	ENST00000522706.5	c.976+25722G>A		intron_variant		5		ENSP00000428635.1
ERICH1	ENST00000523415.5	n.233-15638G>A		intron_variant		2		ENSP00000430296.1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76561 AN: 151800 Hom.: 19504 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.504 AC: 76558 AN: 151918 Hom.: 19497 Cov.: 31 AF XY: 0.500 AC XY: 37133 AN XY: 74238

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.470

Alfa AF: 0.522 Hom.: 2504

Bravo AF: 0.494

Asia WGS AF: 0.463 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1979176; hg19: chr8-592876; COSMIC: COSV72924241; COSMIC: COSV72924241;