rs2022896

Positions:

• chr14-27535424-G-A

Variant summary

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

The NR_148991.1(MIR3171HG):​n.253+121019C>T 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 0.361 in 152,010 control chromosomes in the GnomAD database, including 11,490 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 0.36 (11490 hom., cov: 32)
• Consequence: MIR3171HG NR_148991.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3171HG	NR_148991.1	n.253+121019C>T		intron_variant, non_coding_transcript_variant
MIR3171HG	NR_148992.1	n.358+120914C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3171HG	ENST00000555797.1	n.348+121019C>T		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000556890.1	n.358+120914C>T		intron_variant, non_coding_transcript_variant		1
MIR3171HG	ENST00000553392.5	n.262+121019C>T		intron_variant, non_coding_transcript_variant		3
MIR3171HG	ENST00000554904.5	n.253+121019C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54724 AN: 151888 Hom.: 11463 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.361 AC: 54800 AN: 152010 Hom.: 11490 Cov.: 32 AF XY: 0.358 AC XY: 26610 AN XY: 74296

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.329

Alfa AF: 0.285 Hom.: 3570

Bravo AF: 0.373

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2022896; hg19: chr14-28004630;