rs10930437

Variant names:

• chr2-170724831-G-A
• rs10930437
• ENST00000661242.1:n.1684C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-170724831-G-A
• chr2-170724831-G-C

Variant summary

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

The ENST00000661242.1(ERICH2-DT):​n.1684C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,100 control chromosomes in the GnomAD database, including 36,607 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 0.69 (36607 hom., cov: 32)
• Consequence: ERICH2-DT ENST00000661242.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 8 publications found

Genes affected

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

ENSG00000295294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661242.1. 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
	ERICH2-DT	NR_110185.1		n.286+1212C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERICH2-DT	ENST00000661242.1		n.1684C>T		non_coding_transcript_exon	Exon 4 of 4
	ERICH2-DT	ENST00000662804.1		n.1515C>T		non_coding_transcript_exon	Exon 4 of 4
	ERICH2-DT	ENST00000689466.2		n.1588C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105078 AN: 151982 Hom.: 36570 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.691 AC: 105173 AN: 152100 Hom.: 36607 Cov.: 32 AF XY: 0.692 AC XY: 51455 AN XY: 74356

African (AFR) AF: 0.749 AC: 31058 AN: 41484

American (AMR) AF: 0.656 AC: 10027 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2211 AN: 3472

East Asian (EAS) AF: 0.780 AC: 4038 AN: 5174

South Asian (SAS) AF: 0.667 AC: 3213 AN: 4820

European-Finnish (FIN) AF: 0.688 AC: 7264 AN: 10564

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45081 AN: 67982

Other (OTH) AF: 0.677 AC: 1433 AN: 2116

Alfa AF: 0.673 Hom.: 149120

Bravo AF: 0.696

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.6
DANN	Benign	0.81
PhyloP100		1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10930437;

hg19: chr2-171581341;