rs744531

Positions:

• chr2-111193476-A-G
• chr2-111193476-A-T

Variant summary

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

The ENST00000645030.2(MIR4435-2HG):​n.452+150585T>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 0.63 in 152,016 control chromosomes in the GnomAD database, including 30,672 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 (30672 hom., cov: 32)
• Consequence: MIR4435-2HG ENST00000645030.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 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.452+150585T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95709 AN: 151898 Hom.: 30647 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.630 AC: 95773 AN: 152016 Hom.: 30672 Cov.: 32 AF XY: 0.624 AC XY: 46387 AN XY: 74320

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.620

Alfa AF: 0.585 Hom.: 3356

Bravo AF: 0.630

Asia WGS AF: 0.443 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.80
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: rs744531; hg19: chr2-111951053;