rs4735895

Positions:

• chr8-650729-A-G

Variant summary

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

The XM_047421400.1(ERICH1):​c.*523T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,102 control chromosomes in the GnomAD database, including 36,075 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 0.68 (36075 hom., cov: 34)
• Consequence: ERICH1 XM_047421400.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERICH1	XM_047421400.1	c.*523T>C		3_prime_UTR_variant	7/7		XP_047277356.1
ERICH1	XM_047421404.1	c.*523T>C		3_prime_UTR_variant	6/6		XP_047277360.1
ERICH1	NM_001303100.2	c.1258+17869T>C		intron_variant			NP_001290029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERICH1	ENST00000522706.5	c.976+17869T>C		intron_variant		5		ENSP00000428635	A2
ERICH1	ENST00000523415.5	c.233+17869T>C		intron_variant, NMD_transcript_variant		2		ENSP00000430296

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102775 AN: 151984 Hom.: 36071 Cov.: 34

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.676 AC: 102788 AN: 152102 Hom.: 36075 Cov.: 34 AF XY: 0.674 AC XY: 50071 AN XY: 74340

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.719

Alfa AF: 0.762 Hom.: 58600

Bravo AF: 0.658

Asia WGS AF: 0.632 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.038
DANN	Benign	0.29
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4735895; hg19: chr8-600729;