9-21467713-A-G

Position:

• chr9-21467713-A-G

Variant summary

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

The ENST00000304425.4(MIR31HG):​n.604+9186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,326 control chromosomes in the GnomAD database, including 70,570 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 0.96 (70570 hom., cov: 32)
• Consequence: MIR31HG ENST00000304425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

MIR31HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR31HG	NR_027054.2	n.571+9186T>C		intron_variant
MIR31HG	NR_152877.1	n.312+9186T>C		intron_variant
MIR31HG	NR_152878.1	n.175+9456T>C		intron_variant
MIR31HG	NR_152879.1	n.434+9456T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR31HG	ENST00000304425.4	n.604+9186T>C		intron_variant		2
MIR31HG	ENST00000654736.2	n.394+9186T>C		intron_variant
MIR31HG	ENST00000663833.2	n.246+9456T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146459 AN: 152208 Hom.: 70510 Cov.: 32

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.962 AC: 146578 AN: 152326 Hom.: 70570 Cov.: 32 AF XY: 0.965 AC XY: 71873 AN XY: 74502

Gnomad4 AFR AF: 0.989

Gnomad4 AMR AF: 0.976

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.995

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.977

Alfa AF: 0.944 Hom.: 8426

Bravo AF: 0.966

Asia WGS AF: 0.995 AC: 3459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1888888; hg19: chr9-21467712;