chr8-98076353-C-T

Variant names:

• chr8-98076353-C-T
• rs13278732
• NM_173549.3:c.58+11626C>T

Variant summary

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

The NM_173549.3(ERICH5):​c.58+11626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,390 control chromosomes in the GnomAD database, including 4,837 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 0.25 (4837 hom., cov: 30)
• Consequence: ERICH5 NM_173549.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 12 publications found

Genes affected

ERICH5 (HGNC:26823): (glutamate rich 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173549.3. 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
	ERICH5	NM_173549.3	MANE Select	c.58+11626C>T		intron	N/A	NP_775820.2	Q6P6B1-1
	ERICH5	NM_001170806.2		c.58+11626C>T		intron	N/A	NP_001164277.1	Q6P6B1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH5	ENST00000318528.8	TSL:1 MANE Select	c.58+11626C>T		intron	N/A	ENSP00000315614.3	Q6P6B1-1
	ERICH5	ENST00000890870.1		c.145+8219C>T		intron	N/A	ENSP00000560929.1
	ERICH5	ENST00000890869.1		c.67+11617C>T		intron	N/A	ENSP00000560928.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37212 AN: 151286 Hom.: 4838 Cov.: 30

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0635

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.246 AC: 37229 AN: 151390 Hom.: 4837 Cov.: 30 AF XY: 0.240 AC XY: 17722 AN XY: 73946

African (AFR) AF: 0.256 AC: 10560 AN: 41218

American (AMR) AF: 0.177 AC: 2695 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3466

East Asian (EAS) AF: 0.0636 AC: 327 AN: 5140

South Asian (SAS) AF: 0.230 AC: 1102 AN: 4792

European-Finnish (FIN) AF: 0.179 AC: 1857 AN: 10380

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18914 AN: 67902

Other (OTH) AF: 0.238 AC: 499 AN: 2094

Alfa AF: 0.263 Hom.: 17190

Bravo AF: 0.243

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.41
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: rs13278732; hg19: chr8-99088581;