rs1529806

Positions:

• chr18-47376622-G-A
• chr18-47376622-G-T

Variant summary

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

The NR_147192.1(MIR4527HG):​n.38+90861G>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 0.735 in 152,068 control chromosomes in the GnomAD database, including 41,251 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 0.74 (41251 hom., cov: 32)
• Consequence: MIR4527HG NR_147192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

MIR4527HG (HGNC:31724): (MIR4527 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR4527HG	NR_147192.1	n.38+90861G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4527HG	ENST00000586905.3	n.37+90861G>A		intron_variant, non_coding_transcript_variant		1
MIR4527HG	ENST00000598649.1	n.73+90825G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111713 AN: 151950 Hom.: 41203 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.735 AC: 111820 AN: 152068 Hom.: 41251 Cov.: 32 AF XY: 0.740 AC XY: 54995 AN XY: 74324

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.722

Alfa AF: 0.726 Hom.: 19971

Bravo AF: 0.725

Asia WGS AF: 0.815 AC: 2838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.076
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1529806; hg19: chr18-44902993;