chr8-642876-C-T

Variant names:

• chr8-642876-C-T
• rs1979176
• NM_001303100.2:c.1258+25722G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303100.2. 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
	ERICH1	NM_001303100.2		c.1258+25722G>A		intron	N/A	NP_001290029.1	B4DMI5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH1	ENST00000522706.5	TSL:5	c.976+25722G>A		intron	N/A	ENSP00000428635.1	E5RHA3
	ERICH1	ENST00000523415.5	TSL:2	n.233-15638G>A		intron	N/A	ENSP00000430296.1	H0YBT6

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

African (AFR) AF: 0.438 AC: 18138 AN: 41420

American (AMR) AF: 0.446 AC: 6814 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2680 AN: 5130

South Asian (SAS) AF: 0.481 AC: 2314 AN: 4806

European-Finnish (FIN) AF: 0.519 AC: 5485 AN: 10568

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38017 AN: 67944

Other (OTH) AF: 0.470 AC: 992 AN: 2112

Alfa AF: 0.519 Hom.: 2583

Bravo AF: 0.494

Asia WGS AF: 0.463 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.70
PhyloP100		-0.068
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

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