ENST00000662804.1:n.82+9787C>T

Variant names:

• chr2-170803802-G-A
• rs10432420
• ENST00000662804.1:n.82+9787C>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+9787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,934 control chromosomes in the GnomAD database, including 10,348 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 0.35 (10348 hom., cov: 31)
• Consequence: ERICH2-DT ENST00000662804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 6 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.559 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+9787C>T		intron_variant	Intron 1 of 3
ERICH2-DT	ENST00000728834.1	n.358+13052C>T		intron_variant	Intron 1 of 4
ERICH2-DT	ENST00000728835.1	n.338+13052C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53690 AN: 151816 Hom.: 10335 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.354 AC: 53735 AN: 151934 Hom.: 10348 Cov.: 31 AF XY: 0.355 AC XY: 26349 AN XY: 74262

African (AFR) AF: 0.487 AC: 20167 AN: 41410

American (AMR) AF: 0.296 AC: 4520 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2978 AN: 5170

South Asian (SAS) AF: 0.267 AC: 1288 AN: 4816

European-Finnish (FIN) AF: 0.303 AC: 3192 AN: 10546

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19282 AN: 67954

Other (OTH) AF: 0.346 AC: 730 AN: 2110

Alfa AF: 0.303 Hom.: 3934

Bravo AF: 0.362

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs10432420; hg19: chr2-171660312;