rs6760053

Positions:

• chr2-111175420-C-G

Variant summary

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

The ENST00000645030.2(MIR4435-2HG):​n.453-138498G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,050 control chromosomes in the GnomAD database, including 12,803 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 0.40 (12803 hom., cov: 32)
• Consequence: MIR4435-2HG ENST00000645030.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4435-2HG	ENST00000645030.2	n.453-138498G>C		intron_variant, non_coding_transcript_variant
MIR4435-2HG	ENST00000642191.1	n.340-9820G>C		intron_variant, non_coding_transcript_variant
MIR4435-2HG	ENST00000645051.2	n.450-9790G>C		intron_variant, non_coding_transcript_variant
MIR4435-2HG	ENST00000673798.1	n.652-43165G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61278 AN: 151932 Hom.: 12788 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.403 AC: 61317 AN: 152050 Hom.: 12803 Cov.: 32 AF XY: 0.395 AC XY: 29358 AN XY: 74328

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.367

Alfa AF: 0.440 Hom.: 1884

Bravo AF: 0.394

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.79
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6760053; hg19: chr2-111932997;