rs10432420

Positions:

• chr2-170803802-G-A
• chr2-170803802-G-T

Variant summary

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

The ENST00000662804.1(ERICH2-DT):​n.82+9787C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERICH2-DT	ENST00000662804.1	n.82+9787C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.346

Alfa AF: 0.302 Hom.: 3472

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10432420; hg19: chr2-171660312;