rs986148

chr6-18675307-T-C

Variant summary

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

The NR_149116.1(MIR548A1HG):n.726+1364T>C 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 0.745 in 152,014 control chromosomes in the GnomAD database, including 42,362 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 0.75 (42362 hom., cov: 32)
• Consequence: MIR548A1HG NR_149116.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

Genes affected

MIR548A1HG (HGNC:):

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 = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR548A1HG	NR_149116.1	n.726+1364T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113223 AN: 151896 Hom.: 42338 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.745 AC: 113299 AN: 152014 Hom.: 42362 Cov.: 32 AF XY: 0.746 AC XY: 55419 AN XY: 74300

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.758

Alfa AF: 0.759 Hom.: 19953

Bravo AF: 0.743

Asia WGS AF: 0.779 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.13
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs986148; hg19: chr6-18675538;