ENST00000439362.6:n.544+1858A>T

Variant names:

• chr2-111246290-T-A
• rs2271404
• ENST00000439362.6:n.544+1858A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000439362.6(MIR4435-2HG):​n.544+1858A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: MIR4435-2HG ENST00000439362.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 0 publications found

Genes affected

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

LOC124907867 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439362.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4435-2HG	NR_015395.2		n.2470-6294A>T		intron	N/A
	MIR4435-2HG	NR_136161.1		n.637+1858A>T		intron	N/A
	MIR4435-2HG	NR_136162.1		n.2470-12551A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4435-2HG	ENST00000439362.6	TSL:1	n.544+1858A>T		intron	N/A
	MIR4435-2HG	ENST00000656416.1		n.1812A>T		non_coding_transcript_exon	Exon 5 of 5
	MIR4435-2HG	ENST00000662384.1		n.1694A>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2271404; hg19: chr2-112003867;