rs10498287

Positions:

• chr14-27398580-T-C

Variant summary

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

The ENST00000556890.1(MIR3171HG):​n.359-76439A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 151,402 control chromosomes in the GnomAD database, including 342 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 0.051 (342 hom., cov: 32)
• Consequence: MIR3171HG ENST00000556890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27

Genes affected

MIR3171HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3171HG	NR_148991.1	n.254-76439A>G		intron_variant
MIR3171HG	NR_148992.1	n.359-76439A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3171HG	ENST00000556890.1	n.359-76439A>G		intron_variant		1
MIR3171HG	ENST00000553392.5	n.263-76439A>G		intron_variant		3
MIR3171HG	ENST00000554904.5	n.254-76439A>G		intron_variant		4
MIR3171HG	ENST00000555797.1	n.349-76439A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7692 AN: 151284 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0534

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

GnomAD4 genome AF: 0.0509 AC: 7707 AN: 151402 Hom.: 342 Cov.: 32 AF XY: 0.0527 AC XY: 3897 AN XY: 73966

Gnomad4 AFR AF: 0.0884

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0221

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0552

Alfa AF: 0.0338 Hom.: 44

Bravo AF: 0.0606

Asia WGS AF: 0.118 AC: 408 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498287; hg19: chr14-27867786;