rs135771

Positions:

• chr22-49543536-G-A
• chr22-49543536-G-C

Variant summary

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

The NR_110522.2(MIR3667HG):​n.115+113869C>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 0.161 in 154,486 control chromosomes in the GnomAD database, including 2,484 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 0.16 (2464 hom., cov: 32)
  • Exomes 𝑓: 0.10 (20 hom.)
• Consequence: MIR3667HG NR_110522.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

MIR3667HG (HGNC:28010): (MIR3667 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3667HG	NR_110522.2	n.115+113869C>T		intron_variant, non_coding_transcript_variant
MIR3667HG	NR_110523.2	n.116-102324C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3667HG	ENST00000414287.5	n.101-102324C>T		intron_variant, non_coding_transcript_variant		1
MIR3667HG	ENST00000416411.1	n.54-102324C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24514 AN: 151866 Hom.: 2463 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.102 AC: 255 AN: 2502 Hom.: 20 AF XY: 0.0997 AC XY: 128 AN XY: 1284

Gnomad4 AFR exome AF: 0.171

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.0545

Gnomad4 NFE exome AF: 0.0924

Gnomad4 OTH exome AF: 0.177

GnomAD4 genome AF: 0.162 AC: 24546 AN: 151984 Hom.: 2464 Cov.: 32 AF XY: 0.159 AC XY: 11835 AN XY: 74304

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.153

Alfa AF: 0.152 Hom.: 324

Bravo AF: 0.174

Asia WGS AF: 0.208 AC: 725 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	0.37
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs135771; hg19: chr22-49937184; COSMIC: COSV69267097;