ENST00000642191.1:n.340-27876T>C

Variant names:

• chr2-111193476-A-G
• rs744531
• ENST00000642191.1:n.340-27876T>C

Variant summary

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

The ENST00000642191.1(MIR4435-2HG):​n.340-27876T>C variant causes a intron 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 ENST00000642191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4435-2HG	ENST00000642191.1	n.340-27876T>C		intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645030.2	n.452+150585T>C		intron_variant	Intron 3 of 4
MIR4435-2HG	ENST00000645051.2	n.450-27846T>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.701 AC: 29058 AN: 41448

American (AMR) AF: 0.535 AC: 8178 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2805 AN: 5174

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4820

European-Finnish (FIN) AF: 0.660 AC: 6969 AN: 10560

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42773 AN: 67952

Other (OTH) AF: 0.620 AC: 1310 AN: 2114

Alfa AF: 0.605 Hom.: 8261

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
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs744531; hg19: chr2-111951053;