rs3859501

Variant names:

• chr19-53788157-A-C
• rs3859501
• ENST00000595160.2:n.56T>G

Your query was ambiguous. Multiple possible variants found:

• chr19-53788157-A-C
• chr19-53788157-A-T

Variant summary

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

The ENST00000595160.2(ENSG00000269877):​n.56T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 255,420 control chromosomes in the GnomAD database, including 27,577 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 0.44 (15486 hom., cov: 30)
  • Exomes 𝑓: 0.47 (12091 hom.)
• Consequence: ENSG00000269877 ENST00000595160.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 12 publications found

Genes affected

ENSG00000269877 (HGNC:):

MIR372 (HGNC:31786): (microRNA 372) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904767	XR_007067336.1	n.69T>G		non_coding_transcript_exon_variant	Exon 1 of 2
MIR372	NR_029865.1	n.*201A>C		downstream_gene_variant
MIR372	unassigned_transcript_3400	n.*240A>C		downstream_gene_variant
MIR372	unassigned_transcript_3401	n.*204A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269877	ENST00000595160.2	n.56T>G		non_coding_transcript_exon_variant	Exon 1 of 2	3
ENSG00000269877	ENST00000775521.1	n.45T>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000269564	ENST00000597420.2	n.90-440A>C		intron_variant	Intron 1 of 1	6
MIR372	ENST00000362225.1	n.*201A>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66411 AN: 151662 Hom.: 15483 Cov.: 30

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.500

GnomAD4 exome AF: 0.474 AC: 49136 AN: 103640 Hom.: 12091 Cov.: 0 AF XY: 0.470 AC XY: 26500 AN XY: 56422

African (AFR) AF: 0.263 AC: 882 AN: 3350

American (AMR) AF: 0.448 AC: 2928 AN: 6532

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1202 AN: 2226

East Asian (EAS) AF: 0.532 AC: 2935 AN: 5522

South Asian (SAS) AF: 0.402 AC: 8088 AN: 20140

European-Finnish (FIN) AF: 0.456 AC: 2036 AN: 4462

Middle Eastern (MID) AF: 0.598 AC: 183 AN: 306

European-Non Finnish (NFE) AF: 0.507 AC: 28505 AN: 56252

Other (OTH) AF: 0.490 AC: 2377 AN: 4850

GnomAD4 genome AF: 0.438 AC: 66436 AN: 151780 Hom.: 15486 Cov.: 30 AF XY: 0.433 AC XY: 32103 AN XY: 74186

African (AFR) AF: 0.275 AC: 11380 AN: 41430

American (AMR) AF: 0.459 AC: 6977 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2633 AN: 5114

South Asian (SAS) AF: 0.407 AC: 1958 AN: 4816

European-Finnish (FIN) AF: 0.439 AC: 4621 AN: 10518

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35156 AN: 67914

Other (OTH) AF: 0.503 AC: 1059 AN: 2106

Alfa AF: 0.499 Hom.: 35070

Bravo AF: 0.439

Asia WGS AF: 0.415 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs3859501; hg19: chr19-54291411;