6-18526581-G-T

Variant names:

• chr6-18526581-G-T
• rs6459623
• ENST00000636739.1:n.173+451G>T

Variant summary

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

The ENST00000636739.1(MIR548A1HG):​n.173+451G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 152,178 control chromosomes in the GnomAD database, including 56,243 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 0.86 (56243 hom., cov: 31)
• Consequence: MIR548A1HG ENST00000636739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR548A1HG	NR_149116.1	n.89+3746G>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR548A1HG	ENST00000636739.1	n.173+451G>T		intron_variant	Intron 2 of 4	4
MIR548A1HG	ENST00000637804.1	n.89+3746G>T		intron_variant	Intron 1 of 5	5
MIR548A1HG	ENST00000662927.1	n.101+3746G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130499 AN: 152060 Hom.: 56185 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.858 AC: 130617 AN: 152178 Hom.: 56243 Cov.: 31 AF XY: 0.857 AC XY: 63706 AN XY: 74376

African (AFR) AF: 0.936 AC: 38877 AN: 41538

American (AMR) AF: 0.820 AC: 12525 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2875 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4587 AN: 5168

South Asian (SAS) AF: 0.742 AC: 3569 AN: 4808

European-Finnish (FIN) AF: 0.882 AC: 9345 AN: 10594

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56233 AN: 68006

Other (OTH) AF: 0.855 AC: 1804 AN: 2110

Alfa AF: 0.846 Hom.: 79694

Bravo AF: 0.862

Asia WGS AF: 0.826 AC: 2869 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.66
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs6459623; hg19: chr6-18526812;