rs1456775

Positions:

• chr14-27331794-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_148991.1(MIR3171HG):​n.254-9653T>C 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 0.078 in 151,942 control chromosomes in the GnomAD database, including 1,486 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 0.078 (1486 hom., cov: 32)
• Consequence: MIR3171HG NR_148991.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

Genes affected

MIR3171HG (HGNC:56193): (MIR3171 host gene)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR3171HG	NR_148991.1	n.254-9653T>C		intron_variant, non_coding_transcript_variant
MIR3171HG	NR_148992.1	n.359-9653T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3171HG	ENST00000555797.1	n.349-9653T>C		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000556890.1	n.359-9653T>C		intron_variant, non_coding_transcript_variant		1
MIR3171HG	ENST00000553392.5	n.263-9653T>C		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000554904.5	n.254-9653T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 11843 AN: 151824 Hom.: 1487 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00205

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0780 AC: 11857 AN: 151942 Hom.: 1486 Cov.: 32 AF XY: 0.0745 AC XY: 5536 AN XY: 74266

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.00205

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0610 Hom.: 112

Bravo AF: 0.0887

Asia WGS AF: 0.0130 AC: 44 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	16
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456775; hg19: chr14-27801000;