ENST00000662804.1:n.82+3102G>T

Variant names:

• chr2-170810487-C-A
• rs6755814
• ENST00000662804.1:n.82+3102G>T

Variant summary

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

The ENST00000662804.1(ERICH2-DT):​n.82+3102G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,040 control chromosomes in the GnomAD database, including 30,216 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 0.63 (30216 hom., cov: 32)
• Consequence: ERICH2-DT ENST00000662804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 14 publications found

Genes affected

ERICH2-DT (HGNC:55686): (ERICH2 divergent transcript)

ENSG00000295315 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERICH2-DT	ENST00000662804.1	n.82+3102G>T		intron_variant	Intron 1 of 3
ERICH2-DT	ENST00000728834.1	n.358+6367G>T		intron_variant	Intron 1 of 4
ERICH2-DT	ENST00000728835.1	n.338+6367G>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95504 AN: 151922 Hom.: 30212 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.628 AC: 95550 AN: 152040 Hom.: 30216 Cov.: 32 AF XY: 0.629 AC XY: 46772 AN XY: 74320

African (AFR) AF: 0.611 AC: 25314 AN: 41456

American (AMR) AF: 0.598 AC: 9143 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2248 AN: 3468

East Asian (EAS) AF: 0.791 AC: 4080 AN: 5156

South Asian (SAS) AF: 0.593 AC: 2858 AN: 4816

European-Finnish (FIN) AF: 0.665 AC: 7030 AN: 10572

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42867 AN: 67970

Other (OTH) AF: 0.629 AC: 1328 AN: 2110

Alfa AF: 0.624 Hom.: 51032

Bravo AF: 0.621

Asia WGS AF: 0.652 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.40
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6755814; hg19: chr2-171666997;