2-111246290-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047446748.1(LOC124907867):​c.-2+1858A>G variant causes a intron 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: LOC124907867 XM_047446748.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

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

LOC124907867 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907867	XM_047446748.1	c.-2+1858A>G		intron_variant	Intron 1 of 1		XP_047302704.1
MIR4435-2HG	NR_015395.2	n.2470-6294A>G		intron_variant	Intron 3 of 6
MIR4435-2HG	NR_136161.1	n.637+1858A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4435-2HG	ENST00000439362.6	n.544+1858A>G		intron_variant	Intron 4 of 5	1
MIR4435-2HG	ENST00000656416.1	n.1812A>G		non_coding_transcript_exon_variant	Exon 5 of 5
MIR4435-2HG	ENST00000662384.1	n.1694A>G		non_coding_transcript_exon_variant	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

Gnomad4 AFR AF: 0.0813

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.0954

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.0922

Alfa AF: 0.129 Hom.: 1212

Bravo AF: 0.119

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2271404; hg19: chr2-112003867;