chr2-170810487-C-A

Position:

• chr2-170810487-C-A

Variant summary

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

The ENST00000662804.1(ERICH2-DT):​n.82+3102G>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 0.628 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

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=-0.89).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERICH2-DT	ENST00000662804.1	n.82+3102G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.629

Alfa AF: 0.624 Hom.: 2764

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6755814; hg19: chr2-171666997;