rs10484370

Variant names:

• chr6-18578156-T-C
• rs10484370
• ENST00000637804.1:n.459-12819T>C

Variant summary

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

The ENST00000637804.1(MIR548A1HG):​n.459-12819T>C variant causes a intron 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 ENST00000637804.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• 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=-0.9).
• 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 rank	MANE	Protein	UniProt
MIR548A1HG	NR_149116.1	n.459-12819T>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR548A1HG	ENST00000637804.1	n.459-12819T>C		intron_variant	Intron 3 of 5	5
MIR548A1HG	ENST00000835487.1	n.543-12819T>C		intron_variant	Intron 4 of 5
MIR548A1HG	ENST00000835488.1	n.254-12819T>C		intron_variant	Intron 2 of 3
MIR548A1HG	ENST00000835489.1	n.91-12819T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.279 AC: 11577 AN: 41492

American (AMR) AF: 0.0961 AC: 1470 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3472

East Asian (EAS) AF: 0.0403 AC: 209 AN: 5188

South Asian (SAS) AF: 0.0998 AC: 482 AN: 4830

European-Finnish (FIN) AF: 0.0404 AC: 428 AN: 10606

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0495 AC: 3366 AN: 68022

Other (OTH) AF: 0.109 AC: 230 AN: 2110

Alfa AF: 0.0735 Hom.: 2264

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
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs10484370; hg19: chr6-18578387;