5-31504144-A-G

Position:

• chr5-31504144-A-G

Variant summary

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

The NM_001382508.1(DROSHA):​c.1668+411T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,034 control chromosomes in the GnomAD database, including 8,490 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 0.33 (8490 hom., cov: 32)
• Consequence: DROSHA NM_001382508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

DROSHA (HGNC:17904): (drosha ribonuclease III) This gene encodes a ribonuclease (RNase) III double-stranded RNA-specific ribonuclease and subunit of the microprocessor protein complex, which catalyzes the initial processing step of microRNA (miRNA) synthesis. The encoded protein cleaves the stem loop structure from the primary microRNA (pri-miRNA) in the nucleus, yielding the precursor miRNA (pre-miRNA), which is then exported to the cytoplasm for further processing. In a human cell line lacking a functional copy of this gene, canonical miRNA synthesis is reduced. Somatic mutations in this gene have been observed in human patients with kidney cancer. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DROSHA	NM_001382508.1	c.1668+411T>C		intron_variant		ENST00000344624.8	NP_001369437.1
DROSHA	NM_001100412.2	c.1557+411T>C		intron_variant			NP_001093882.1
DROSHA	NM_013235.5	c.1668+411T>C		intron_variant			NP_037367.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DROSHA	ENST00000344624.8	c.1668+411T>C		intron_variant		5	NM_001382508.1	ENSP00000339845	P4
DROSHA	ENST00000511367.6	c.1668+411T>C		intron_variant		1		ENSP00000425979	P4
DROSHA	ENST00000512076.1	c.952+411T>C		intron_variant		1		ENSP00000422745
DROSHA	ENST00000513349.5	c.1557+411T>C		intron_variant		1		ENSP00000424161	A1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50028 AN: 151916 Hom.: 8492 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.329 AC: 50051 AN: 152034 Hom.: 8490 Cov.: 32 AF XY: 0.330 AC XY: 24517 AN XY: 74326

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.338

Alfa AF: 0.335 Hom.: 14398

Bravo AF: 0.330

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7737174; hg19: chr5-31504251;