chr9-21471500-C-T

Position:

• chr9-21471500-C-T

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.604+5399G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,014 control chromosomes in the GnomAD database, including 28,011 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 0.60 (28011 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

MIR31HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.571+5399G>A		intron_variant
MIR31HG	NR_152877.1	n.312+5399G>A		intron_variant
MIR31HG	NR_152878.1	n.175+5669G>A		intron_variant
MIR31HG	NR_152879.1	n.434+5669G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.604+5399G>A		intron_variant		2
MIR31HG	ENST00000654736.2	n.394+5399G>A		intron_variant
MIR31HG	ENST00000663833.2	n.246+5669G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91635 AN: 151896 Hom.: 27995 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.603 AC: 91689 AN: 152014 Hom.: 28011 Cov.: 32 AF XY: 0.605 AC XY: 44975 AN XY: 74298

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.612

Alfa AF: 0.602 Hom.: 12579

Bravo AF: 0.610

Asia WGS AF: 0.793 AC: 2753 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412395; hg19: chr9-21471499;