rs1954668

Variant names:

• chr14-27463132-A-G
• rs1954668
• ENST00000556890.1:n.359-140991T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556890.1(MIR3171HG):​n.359-140991T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,944 control chromosomes in the GnomAD database, including 23,208 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 0.53 (23208 hom., cov: 32)
• Consequence: MIR3171HG ENST00000556890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 3 publications found

Genes affected

MIR3171HG (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3171HG	NR_148991.1	n.254-140991T>C		intron_variant	Intron 2 of 2
MIR3171HG	NR_148992.1	n.359-140991T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3171HG	ENST00000556890.1	n.359-140991T>C		intron_variant	Intron 2 of 2	1
MIR3171HG	ENST00000553392.5	n.263-140991T>C		intron_variant	Intron 2 of 5	3
MIR3171HG	ENST00000554904.5	n.254-140991T>C		intron_variant	Intron 2 of 2	4
MIR3171HG	ENST00000555797.1	n.349-140991T>C		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80506 AN: 151826 Hom.: 23198 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.530 AC: 80523 AN: 151944 Hom.: 23208 Cov.: 32 AF XY: 0.530 AC XY: 39386 AN XY: 74262

African (AFR) AF: 0.293 AC: 12131 AN: 41470

American (AMR) AF: 0.619 AC: 9429 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2576 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1927 AN: 5148

South Asian (SAS) AF: 0.572 AC: 2749 AN: 4808

European-Finnish (FIN) AF: 0.587 AC: 6202 AN: 10560

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43592 AN: 67940

Other (OTH) AF: 0.578 AC: 1218 AN: 2108

Alfa AF: 0.576 Hom.: 3442

Bravo AF: 0.520

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1954668; hg19: chr14-27932338;