ENST00000642191.1:n.340-8244A>G

Variant names:

• chr2-111173844-T-C
• rs726430
• ENST00000642191.1:n.340-8244A>G

Variant summary

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

The ENST00000642191.1(MIR4435-2HG):​n.340-8244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,190 control chromosomes in the GnomAD database, including 1,945 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 0.15 (1945 hom., cov: 33)
• Consequence: MIR4435-2HG ENST00000642191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 11 publications found

Genes affected

MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 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
MIR4435-2HG	ENST00000642191.1	n.340-8244A>G		intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645030.2	n.453-136922A>G		intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645051.2	n.450-8214A>G		intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000673798.1	n.652-41589A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22940 AN: 152072 Hom.: 1940 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0644

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.151 AC: 22963 AN: 152190 Hom.: 1945 Cov.: 33 AF XY: 0.146 AC XY: 10842 AN XY: 74390

African (AFR) AF: 0.116 AC: 4830 AN: 41530

American (AMR) AF: 0.104 AC: 1595 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0644 AC: 223 AN: 3464

East Asian (EAS) AF: 0.247 AC: 1280 AN: 5174

South Asian (SAS) AF: 0.0870 AC: 419 AN: 4818

European-Finnish (FIN) AF: 0.154 AC: 1635 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12495 AN: 67984

Other (OTH) AF: 0.124 AC: 262 AN: 2110

Alfa AF: 0.171 Hom.: 2810

Bravo AF: 0.149

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.54
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs726430; hg19: chr2-111931421;