chr6-18578156-T-C

Position:

• chr6-18578156-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.459-12819T>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 0.118 in 152,220 control chromosomes in the GnomAD database, including 1,873 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 0.12 (1873 hom., cov: 33)
• Consequence: MIR548A1HG NR_149116.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

MIR548A1HG (HGNC:53539): (MIR548A1 host gene)

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 (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR548A1HG	NR_149116.1	n.459-12819T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR548A1HG	ENST00000637804.1	n.459-12819T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17938 AN: 152102 Hom.: 1875 Cov.: 33

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.118 AC: 17952 AN: 152220 Hom.: 1873 Cov.: 33 AF XY: 0.116 AC XY: 8652 AN XY: 74432

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.0403

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0495

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0595 Hom.: 760

Bravo AF: 0.128

Asia WGS AF: 0.0830 AC: 287 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484370; hg19: chr6-18578387;