rs243034

Positions:

• chr2-60375757-C-T

Variant summary

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

The NR_132992.1(MIR4432HG):​n.70+15549G>A 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 0.568 in 151,912 control chromosomes in the GnomAD database, including 25,136 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 0.57 (25136 hom., cov: 31)
• Consequence: MIR4432HG NR_132992.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR4432HG	NR_132992.1	n.70+15549G>A		intron_variant, non_coding_transcript_variant
MIR4432HG	NR_132991.1	n.212+2745G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4432HG	ENST00000650395.1	n.389-5720G>A		intron_variant, non_coding_transcript_variant
MIR4432HG	ENST00000441598.2	n.212+2745G>A		intron_variant, non_coding_transcript_variant		3
MIR4432HG	ENST00000453476.1	n.70+15549G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86284 AN: 151794 Hom.: 25114 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.568 AC: 86358 AN: 151912 Hom.: 25136 Cov.: 31 AF XY: 0.562 AC XY: 41728 AN XY: 74254

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.566

Alfa AF: 0.592 Hom.: 40307

Bravo AF: 0.554

Asia WGS AF: 0.398 AC: 1381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243034; hg19: chr2-60602892;