rs13293512

Variant names:

• chr9-94167461-T-C
• rs13293512
• ENST00000602703.2:n.108+1080T>C

Variant summary

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

The ENST00000602703.2(MIRLET7A1HG):​n.108+1080T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,250 control chromosomes in the GnomAD database, including 5,685 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 0.25 (5685 hom., cov: 33)
• Consequence: MIRLET7A1HG ENST00000602703.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 29 publications found

Genes affected

MIRLET7A1HG (HGNC:53970): (miRlet-7a-1/let-7f-1/let-7d cluster host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIRLET7A1HG	NR_170274.1	n.124+1080T>C		intron_variant	Intron 1 of 1
MIRLET7A1HG	NR_170275.1	n.124+1080T>C		intron_variant	Intron 1 of 1
MIRLET7A1HG	NR_170276.1	n.124+1080T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIRLET7A1HG	ENST00000602703.2	n.108+1080T>C		intron_variant	Intron 1 of 1	3
MIRLET7A1HG	ENST00000652620.1	n.116+1080T>C		intron_variant	Intron 1 of 4
MIRLET7A1HG	ENST00000652769.2	n.124+1080T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37336 AN: 152132 Hom.: 5687 Cov.: 33

Gnomad AFR AF: 0.0608

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.245 AC: 37339 AN: 152250 Hom.: 5685 Cov.: 33 AF XY: 0.247 AC XY: 18357 AN XY: 74450

African (AFR) AF: 0.0606 AC: 2519 AN: 41564

American (AMR) AF: 0.272 AC: 4167 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2288 AN: 5192

South Asian (SAS) AF: 0.353 AC: 1702 AN: 4822

European-Finnish (FIN) AF: 0.317 AC: 3354 AN: 10590

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21430 AN: 67998

Other (OTH) AF: 0.277 AC: 586 AN: 2112

Alfa AF: 0.261 Hom.: 807

Bravo AF: 0.235

Asia WGS AF: 0.341 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.75
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs13293512; hg19: chr9-96929743;