2-111191750-G-C

Variant names:

• chr2-111191750-G-C
• rs6738028
• ENST00000642191.1:n.340-26150C>G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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.340-26150C>G		intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645030.2	n.452+152311C>G		intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645051.2	n.450-26120C>G		intron_variant	Intron 3 of 4

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

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.604

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6738028; hg19: chr2-111949327;