chr2-111246290-T-C

Variant names:

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

Variant summary

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

The ENST00000656416.1(MIR4435-2HG):​n.1812A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,228 control chromosomes in the GnomAD database, including 1,346 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 0.12 (1346 hom., cov: 32)
• Consequence: MIR4435-2HG ENST00000656416.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 10 publications found

Genes affected

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

LOC124907867 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656416.1. 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>G		intron	N/A
	MIR4435-2HG	NR_136161.1		n.637+1858A>G		intron	N/A
	MIR4435-2HG	NR_136162.1		n.2470-12551A>G		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>G		intron	N/A
	MIR4435-2HG	ENST00000656416.1		n.1812A>G		non_coding_transcript_exon	Exon 5 of 5
	MIR4435-2HG	ENST00000662384.1		n.1694A>G		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18727 AN: 152110 Hom.: 1341 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0866

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.123 AC: 18750 AN: 152228 Hom.: 1346 Cov.: 32 AF XY: 0.121 AC XY: 9025 AN XY: 74428

African (AFR) AF: 0.0813 AC: 3377 AN: 41546

American (AMR) AF: 0.0865 AC: 1324 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0954 AC: 331 AN: 3468

East Asian (EAS) AF: 0.264 AC: 1364 AN: 5174

South Asian (SAS) AF: 0.0657 AC: 317 AN: 4826

European-Finnish (FIN) AF: 0.170 AC: 1800 AN: 10594

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9954 AN: 67994

Other (OTH) AF: 0.0922 AC: 195 AN: 2116

Alfa AF: 0.134 Hom.: 3821

Bravo AF: 0.119

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.38
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;