8-650729-A-G

Variant names:

• chr8-650729-A-G
• rs4735895
• XM_047421400.1:c.*523T>C

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+17869T>C variant causes a intron 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 NM_001303100.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 25 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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+17869T>C		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+17869T>C		intron	N/A	ENSP00000428635.1	E5RHA3
	ERICH1	ENST00000523415.5	TSL:2	n.232+17869T>C		intron	N/A	ENSP00000430296.1	H0YBT6

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

African (AFR) AF: 0.490 AC: 20330 AN: 41502

American (AMR) AF: 0.629 AC: 9613 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2833 AN: 3472

East Asian (EAS) AF: 0.563 AC: 2890 AN: 5130

South Asian (SAS) AF: 0.742 AC: 3573 AN: 4818

European-Finnish (FIN) AF: 0.729 AC: 7713 AN: 10586

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53261 AN: 67990

Other (OTH) AF: 0.719 AC: 1518 AN: 2110

Alfa AF: 0.748 Hom.: 79127

Bravo AF: 0.658

Asia WGS AF: 0.632 AC: 2201 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	0.038
DANN	Benign	0.29
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
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: rs4735895; hg19: chr8-600729;