ENST00000416202.6:n.1637G>A

Variant names:

• chr22-46058328-G-A
• rs3744749
• ENST00000416202.6:n.1637G>A

Variant summary

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

The ENST00000416202.6(MIRLET7BHG):​n.1637G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,124 control chromosomes in the GnomAD database, including 4,121 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 0.20 (4121 hom., cov: 33)
• Consequence: MIRLET7BHG ENST00000416202.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 16 publications found

Genes affected

MIRLET7BHG (HGNC:37189): (MIRLET7B host gene)

PRR34-AS1 (HGNC:50499): (PRR34 antisense RNA 1)

LOC124905135 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRR34-AS1	NR_027034.1	n.1441G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC124905135	XM_047441696.1	c.-5555+13321G>A		intron_variant	Intron 1 of 1		XP_047297652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIRLET7BHG	ENST00000416202.6	n.1637G>A		non_coding_transcript_exon_variant	Exon 3 of 3	2
MIRLET7BHG	ENST00000794313.1	n.1461G>A		non_coding_transcript_exon_variant	Exon 3 of 3
MIRLET7BHG	ENST00000794314.1	n.1374G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29826 AN: 152004 Hom.: 4098 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.197 AC: 29906 AN: 152124 Hom.: 4121 Cov.: 33 AF XY: 0.192 AC XY: 14279 AN XY: 74386

African (AFR) AF: 0.391 AC: 16213 AN: 41464

American (AMR) AF: 0.140 AC: 2141 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3468

East Asian (EAS) AF: 0.128 AC: 663 AN: 5172

South Asian (SAS) AF: 0.143 AC: 688 AN: 4824

European-Finnish (FIN) AF: 0.0759 AC: 804 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7975 AN: 67992

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.141 Hom.: 3236

Bravo AF: 0.211

Asia WGS AF: 0.130 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.92
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3744749; hg19: chr22-46454208;