rs13293512

Positions:

• chr9-94167461-T-C

Variant summary

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

The NR_170278.1(MIRLET7A1HG):​n.124+1080T>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 0.245 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 NR_170278.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MIRLET7A1HG	NR_170278.1	n.124+1080T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIRLET7A1HG	ENST00000710611.1	n.108+1080T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0606

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.277

Alfa AF: 0.269 Hom.: 805

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13293512; hg19: chr9-96929743;