rs2877832

chr14-27330971-C-T

Variant summary

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

The NR_148991.1(MIR3171HG):n.254-8830G>A 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 0.0782 in 152,034 control chromosomes in the GnomAD database, including 561 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 (561 hom., cov: 32)
• Consequence: MIR3171HG NR_148991.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

Genes affected

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

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 = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3171HG	NR_148991.1	n.254-8830G>A		intron_variant, non_coding_transcript_variant
MIR3171HG	NR_148992.1	n.359-8830G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3171HG	ENST00000555797.1	n.349-8830G>A		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000556890.1	n.359-8830G>A		intron_variant, non_coding_transcript_variant		1
MIR3171HG	ENST00000553392.5	n.263-8830G>A		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000554904.5	n.254-8830G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0782 AC: 11885 AN: 151916 Hom.: 560 Cov.: 32

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.0575

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0747

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

GnomAD4 genome AF: 0.0782 AC: 11885 AN: 152034 Hom.: 561 Cov.: 32 AF XY: 0.0745 AC XY: 5534 AN XY: 74312

Gnomad4 AFR AF: 0.0342

Gnomad4 AMR AF: 0.0567

Gnomad4 ASJ AF: 0.0737

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0789

Gnomad4 FIN AF: 0.0575

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.101 Hom.: 963

Bravo AF: 0.0768

Asia WGS AF: 0.0720 AC: 248 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.81
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2877832; hg19: chr14-27800177;