chr5-88567015-C-T

Position:

• chr5-88567015-C-T

Variant summary

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

The NR_015436.2(MIR9-2HG):​n.283-24945G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,160 control chromosomes in the GnomAD database, including 633 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 0.043 (633 hom., cov: 32)
• Consequence: MIR9-2HG NR_015436.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

LINC00461 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR9-2HG	NR_015436.2	n.283-24945G>A		intron_variant
MIR9-2HG	NR_152235.1	n.219-24945G>A		intron_variant
MIR9-2HG	NR_152238.1	n.216-24945G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00461	ENST00000502301.5	n.213-24945G>A		intron_variant		4
LINC00461	ENST00000506014.5	n.149-24945G>A		intron_variant		4
LINC00461	ENST00000506664.7	n.103-24945G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6474 AN: 152042 Hom.: 632 Cov.: 32

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0460

Gnomad ASJ AF: 0.00462

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0167

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0426 AC: 6475 AN: 152160 Hom.: 633 Cov.: 32 AF XY: 0.0470 AC XY: 3500 AN XY: 74402

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.00462

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0167

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0281 Hom.: 30

Bravo AF: 0.0433

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977669; hg19: chr5-87862833;