rs11894442

Positions:

• chr2-60429883-T-C

Variant summary

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

The ENST00000650395.1(MIR4432HG):​n.265+9681A>G 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 0.509 in 151,972 control chromosomes in the GnomAD database, including 20,097 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 0.51 (20097 hom., cov: 32)
• Consequence: MIR4432HG ENST00000650395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

MIR4432HG (HGNC:52005): (MIR4432 host gene)

LOC124906010 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906010	XM_047446573.1	c.331+9389A>G		intron_variant
LOC124906010	XR_007086328.1	n.606+3570A>G		intron_variant, non_coding_transcript_variant
LOC124906010	XR_007086329.1	n.531+3570A>G		intron_variant, non_coding_transcript_variant
LOC124906010	XR_007086331.1	n.365+3570A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4432HG	ENST00000650395.1	n.265+9681A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77315 AN: 151852 Hom.: 20069 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.509 AC: 77393 AN: 151972 Hom.: 20097 Cov.: 32 AF XY: 0.511 AC XY: 37963 AN XY: 74274

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.457

Alfa AF: 0.482 Hom.: 8487

Bravo AF: 0.512

Asia WGS AF: 0.564 AC: 1957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11894442; hg19: chr2-60657018;