9-94175196-C-T

Position:

• chr9-94175196-C-T

Variant summary

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

The ENST00000602703.1(MIRLET7A1HG):​n.93+8815C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,106 control chromosomes in the GnomAD database, including 20,174 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 0.48 (20174 hom., cov: 33)
• Consequence: MIRLET7A1HG ENST00000602703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

Genes affected

MIRLET7A1HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIRLET7A1HG	NR_170274.1	n.125-669C>T		intron_variant
MIRLET7A1HG	NR_170275.1	n.124+8815C>T		intron_variant
MIRLET7A1HG	NR_170276.1	n.125-669C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIRLET7A1HG	ENST00000602703.1	n.93+8815C>T		intron_variant		3
MIRLET7A1HG	ENST00000652620.1	n.117-669C>T		intron_variant
MIRLET7A1HG	ENST00000652769.2	n.125-669C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73749 AN: 151988 Hom.: 20184 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.485 AC: 73746 AN: 152106 Hom.: 20174 Cov.: 33 AF XY: 0.485 AC XY: 36100 AN XY: 74364

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.546

Alfa AF: 0.503 Hom.: 3514

Bravo AF: 0.467

Asia WGS AF: 0.491 AC: 1706 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10761322; hg19: chr9-96937478;