rs1456775

Variant names:

• chr14-27331794-A-G
• rs1456775
• ENST00000556890.1:n.359-9653T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000556890.1(MIR3171HG):​n.359-9653T>C variant causes a intron 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 ENST00000556890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 0 publications found

Genes affected

MIR3171HG (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MIR3171HG	NR_148991.1	n.254-9653T>C		intron_variant	Intron 2 of 2
MIR3171HG	NR_148992.1	n.359-9653T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3171HG	ENST00000556890.1	n.359-9653T>C		intron_variant	Intron 2 of 2	1
MIR3171HG	ENST00000553392.5	n.263-9653T>C		intron_variant	Intron 2 of 5	3
MIR3171HG	ENST00000554904.5	n.254-9653T>C		intron_variant	Intron 2 of 2	4
MIR3171HG	ENST00000555797.1	n.349-9653T>C		intron_variant	Intron 3 of 3	3

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

African (AFR) AF: 0.264 AC: 10955 AN: 41486

American (AMR) AF: 0.0353 AC: 539 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 98 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00124 AC: 6 AN: 4828

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00205 AC: 139 AN: 67812

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0708 Hom.: 145

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
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1456775; hg19: chr14-27801000;