2-111173844-T-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642191.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4435-2HG	ENST00000642191.1		n.340-8244A>G		intron	N/A
	MIR4435-2HG	ENST00000645030.2		n.453-136922A>G		intron	N/A
	MIR4435-2HG	ENST00000645051.2		n.450-8214A>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs726430;

hg19: chr2-111931421;