rs30222

chr16-14315801-G-A

Variant summary

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

The NR_170633.1(MIR193BHG):n.152-10212G>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 0.72 in 152,208 control chromosomes in the GnomAD database, including 40,827 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 0.72 (40827 hom., cov: 33)
• Consequence: MIR193BHG NR_170633.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

MIR193BHG (HGNC:51945): (MIR193b-365a host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR193BHG	NR_170633.1	n.152-10212G>A		intron_variant, non_coding_transcript_variant
MIR193BHG	NR_132983.2	n.355-10212G>A		intron_variant, non_coding_transcript_variant
MIR193BHG	NR_132984.2	n.294-10212G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR193BHG	ENST00000641433.1	n.311-10212G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109508 AN: 152090 Hom.: 40768 Cov.: 33

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.720 AC: 109629 AN: 152208 Hom.: 40827 Cov.: 33 AF XY: 0.720 AC XY: 53557 AN XY: 74396

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.727

Alfa AF: 0.692 Hom.: 6968

Bravo AF: 0.727

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.12
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30222; hg19: chr16-14409658;