rs3805516

Variant names:

• chr5-31420563-A-G
• rs3805516
• NM_001382508.1:c.3525+709T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-31420563-A-G
• chr5-31420563-A-T

Variant summary

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

The NM_001382508.1(DROSHA):​c.3525+709T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,006 control chromosomes in the GnomAD database, including 7,756 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 0.30 (7756 hom., cov: 32)
• Consequence: DROSHA NM_001382508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DROSHA	NM_001382508.1	c.3525+709T>C		intron_variant	Intron 30 of 35	ENST00000344624.8	NP_001369437.1
DROSHA	NM_013235.5	c.3525+709T>C		intron_variant	Intron 29 of 34		NP_037367.3
DROSHA	NM_001100412.2	c.3414+709T>C		intron_variant	Intron 29 of 34		NP_001093882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DROSHA	ENST00000344624.8	c.3525+709T>C		intron_variant	Intron 30 of 35	5	NM_001382508.1	ENSP00000339845.3
DROSHA	ENST00000511367.6	c.3525+709T>C		intron_variant	Intron 29 of 34	1		ENSP00000425979.2
DROSHA	ENST00000513349.5	c.3414+709T>C		intron_variant	Intron 29 of 34	1		ENSP00000424161.1
DROSHA	ENST00000511778.5	n.641+709T>C		intron_variant	Intron 2 of 7	3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45125 AN: 151888 Hom.: 7736 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.297 AC: 45191 AN: 152006 Hom.: 7756 Cov.: 32 AF XY: 0.299 AC XY: 22250 AN XY: 74316

African (AFR) AF: 0.452 AC: 18713 AN: 41422

American (AMR) AF: 0.308 AC: 4705 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1026 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2572 AN: 5170

South Asian (SAS) AF: 0.346 AC: 1667 AN: 4824

European-Finnish (FIN) AF: 0.204 AC: 2155 AN: 10566

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13402 AN: 67958

Other (OTH) AF: 0.290 AC: 612 AN: 2112

Alfa AF: 0.240 Hom.: 2856

Bravo AF: 0.311

Asia WGS AF: 0.459 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.2
DANN	Benign	0.81
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3805516; hg19: chr5-31420670;