rs10739971

Variant names:

• chr9-94175398-G-A
• rs10739971
• ENST00000602703.2:n.108+9017G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-94175398-G-A
• chr9-94175398-G-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+9017G>A 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 152,076 control chromosomes in the GnomAD database, including 5,664 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 (5664 hom., cov: 32)
• Consequence: MIRLET7A1HG ENST00000602703.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 23 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIRLET7A1HG	NR_170274.1	n.125-467G>A		intron_variant	Intron 1 of 1
MIRLET7A1HG	NR_170275.1	n.124+9017G>A		intron_variant	Intron 1 of 1
MIRLET7A1HG	NR_170276.1	n.125-467G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIRLET7A1HG	ENST00000602703.2	n.108+9017G>A		intron_variant	Intron 1 of 1	3
MIRLET7A1HG	ENST00000652620.1	n.117-467G>A		intron_variant	Intron 1 of 4
MIRLET7A1HG	ENST00000652769.2	n.125-467G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37275 AN: 151958 Hom.: 5666 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.363

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: 0.237

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: 37278 AN: 152076 Hom.: 5664 Cov.: 32 AF XY: 0.246 AC XY: 18314 AN XY: 74318

African (AFR) AF: 0.0607 AC: 2520 AN: 41540

American (AMR) AF: 0.272 AC: 4155 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2277 AN: 5170

South Asian (SAS) AF: 0.352 AC: 1701 AN: 4826

European-Finnish (FIN) AF: 0.317 AC: 3337 AN: 10526

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21408 AN: 67954

Other (OTH) AF: 0.278 AC: 587 AN: 2114

Alfa AF: 0.244 Hom.: 1987

Bravo AF: 0.235

Asia WGS AF: 0.340 AC: 1182 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10739971; hg19: chr9-96937680;