chr2-111191750-G-C

Variant names:

• chr2-111191750-G-C
• rs6738028
• ENST00000642191.1:n.340-26150C>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.340-26150C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 152,018 control chromosomes in the GnomAD database, including 31,729 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 (31729 hom., cov: 31)
• Consequence: MIR4435-2HG ENST00000642191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 24 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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.340-26150C>G		intron	N/A
	MIR4435-2HG	ENST00000645030.2		n.452+152311C>G		intron	N/A
	MIR4435-2HG	ENST00000645051.2		n.450-26120C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96200 AN: 151900 Hom.: 31678 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.633 AC: 96299 AN: 152018 Hom.: 31729 Cov.: 31 AF XY: 0.625 AC XY: 46420 AN XY: 74298

African (AFR) AF: 0.806 AC: 33435 AN: 41482

American (AMR) AF: 0.518 AC: 7911 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1861 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2753 AN: 5162

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4812

European-Finnish (FIN) AF: 0.593 AC: 6246 AN: 10534

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.596 AC: 40478 AN: 67966

Other (OTH) AF: 0.604 AC: 1276 AN: 2112

Alfa AF: 0.597 Hom.: 15162

Bravo AF: 0.641

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.46
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6738028; hg19: chr2-111949327;